Starting phenix.real_space_refine on Sat Mar 23 09:12:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqu_24636/03_2024/7rqu_24636_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqu_24636/03_2024/7rqu_24636.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqu_24636/03_2024/7rqu_24636_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqu_24636/03_2024/7rqu_24636_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqu_24636/03_2024/7rqu_24636_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqu_24636/03_2024/7rqu_24636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqu_24636/03_2024/7rqu_24636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqu_24636/03_2024/7rqu_24636_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqu_24636/03_2024/7rqu_24636_trim_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.140 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 24 5.49 5 S 88 5.16 5 Na 2 4.78 5 C 12500 2.51 5 N 2980 2.21 5 O 3440 1.98 5 H 16568 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35602 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 8623 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 587} Chain breaks: 5 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 225 Chain: "C" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 8623 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 587} Chain breaks: 5 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 225 Chain: "B" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 8623 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 587} Chain breaks: 5 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 225 Chain: "D" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 8623 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 587} Chain breaks: 5 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 225 Chain: "A" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 279 Unusual residues: {' NA': 2, '6EU': 1, '6OU': 5, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'YFP:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 4} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 277 Unusual residues: {'6EU': 1, '6OU': 5, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'YFP:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 4} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 277 Unusual residues: {'6EU': 1, '6OU': 5, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'YFP:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 277 Unusual residues: {'6EU': 1, '6OU': 5, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'YFP:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 26 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA A 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA C 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA B 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 204 " occ=0.50 Time building chain proxies: 15.53, per 1000 atoms: 0.44 Number of scatterers: 35602 At special positions: 0 Unit cell: (132.84, 132.84, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 88 16.00 P 24 15.00 Na 2 11.00 O 3440 8.00 N 2980 7.00 C 12500 6.00 H 16568 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.77 Conformation dependent library (CDL) restraints added in 3.7 seconds 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 8 sheets defined 57.5% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.92 Creating SS restraints... Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 127 through 138 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 416 through 429 removed outlier: 4.275A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.252A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 532 Processing helix chain 'A' and resid 537 through 558 removed outlier: 4.242A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLY A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.726A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 removed outlier: 3.787A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 692 through 712 Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 127 through 138 Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 416 through 429 removed outlier: 4.274A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 503 through 509 removed outlier: 4.252A pdb=" N PHE C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 532 Processing helix chain 'C' and resid 537 through 558 removed outlier: 4.242A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLY C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.726A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 removed outlier: 3.786A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 692 through 712 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 127 through 138 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 416 through 429 removed outlier: 4.275A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 503 through 509 removed outlier: 4.252A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 532 Processing helix chain 'B' and resid 537 through 558 removed outlier: 4.242A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLY B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.725A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 3.786A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 692 through 712 Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 127 through 138 Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 416 through 429 removed outlier: 4.275A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 503 through 509 removed outlier: 4.251A pdb=" N PHE D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 532 Processing helix chain 'D' and resid 537 through 558 removed outlier: 4.243A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLY D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 3.725A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 642 removed outlier: 3.787A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 692 through 712 Processing sheet with id= A, first strand: chain 'A' and resid 744 through 747 removed outlier: 6.326A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 724 through 727 Processing sheet with id= C, first strand: chain 'C' and resid 744 through 747 removed outlier: 6.326A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 724 through 727 Processing sheet with id= E, first strand: chain 'B' and resid 744 through 747 removed outlier: 6.326A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 724 through 727 Processing sheet with id= G, first strand: chain 'D' and resid 744 through 747 removed outlier: 6.325A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 724 through 727 948 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.10 Time building geometry restraints manager: 27.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16544 1.03 - 1.23: 194 1.23 - 1.42: 7970 1.42 - 1.62: 11068 1.62 - 1.82: 208 Bond restraints: 35984 Sorted by residual: bond pdb=" CAS 6EU B 906 " pdb=" CAX 6EU B 906 " ideal model delta sigma weight residual 1.334 1.614 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" CAS 6EU C 901 " pdb=" CAX 6EU C 901 " ideal model delta sigma weight residual 1.334 1.613 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" CAS 6EU A 901 " pdb=" CAX 6EU A 901 " ideal model delta sigma weight residual 1.334 1.613 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" CAS 6EU D 906 " pdb=" CAX 6EU D 906 " ideal model delta sigma weight residual 1.334 1.613 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" CAW 6EU B 906 " pdb=" CBA 6EU B 906 " ideal model delta sigma weight residual 1.339 1.524 -0.185 2.00e-02 2.50e+03 8.54e+01 ... (remaining 35979 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 327 105.81 - 112.87: 39121 112.87 - 119.93: 10548 119.93 - 126.99: 13737 126.99 - 134.04: 179 Bond angle restraints: 63912 Sorted by residual: angle pdb=" N TRP B 749 " pdb=" CA TRP B 749 " pdb=" C TRP B 749 " ideal model delta sigma weight residual 111.14 117.73 -6.59 1.08e+00 8.57e-01 3.72e+01 angle pdb=" N TRP A 749 " pdb=" CA TRP A 749 " pdb=" C TRP A 749 " ideal model delta sigma weight residual 111.14 117.71 -6.57 1.08e+00 8.57e-01 3.70e+01 angle pdb=" N TRP C 749 " pdb=" CA TRP C 749 " pdb=" C TRP C 749 " ideal model delta sigma weight residual 111.14 117.71 -6.57 1.08e+00 8.57e-01 3.70e+01 angle pdb=" N TRP D 749 " pdb=" CA TRP D 749 " pdb=" C TRP D 749 " ideal model delta sigma weight residual 111.14 117.70 -6.56 1.08e+00 8.57e-01 3.69e+01 angle pdb=" C39 6OU D 901 " pdb=" C40 6OU D 901 " pdb=" C41 6OU D 901 " ideal model delta sigma weight residual 127.60 109.77 17.83 3.00e+00 1.11e-01 3.53e+01 ... (remaining 63907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 17178 35.21 - 70.43: 608 70.43 - 105.64: 57 105.64 - 140.86: 42 140.86 - 176.07: 23 Dihedral angle restraints: 17908 sinusoidal: 9348 harmonic: 8560 Sorted by residual: dihedral pdb=" C19 6OU A 905 " pdb=" C20 6OU A 905 " pdb=" C21 6OU A 905 " pdb=" O22 6OU A 905 " ideal model delta sinusoidal sigma weight residual 301.00 124.93 176.07 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU A 903 " pdb=" C20 6OU A 903 " pdb=" O30 6OU A 903 " pdb=" C31 6OU A 903 " ideal model delta sinusoidal sigma weight residual 212.33 39.75 172.58 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C19 6OU D 908 " pdb=" C20 6OU D 908 " pdb=" O30 6OU D 908 " pdb=" C31 6OU D 908 " ideal model delta sinusoidal sigma weight residual 212.33 39.75 172.58 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 17905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2834 0.092 - 0.184: 73 0.184 - 0.276: 27 0.276 - 0.368: 22 0.368 - 0.460: 16 Chirality restraints: 2972 Sorted by residual: chirality pdb=" C2 LBN A 908 " pdb=" C1 LBN A 908 " pdb=" C3 LBN A 908 " pdb=" O7 LBN A 908 " both_signs ideal model delta sigma weight residual False -2.36 -2.82 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" C2 LBN D 907 " pdb=" C1 LBN D 907 " pdb=" C3 LBN D 907 " pdb=" O7 LBN D 907 " both_signs ideal model delta sigma weight residual False -2.36 -2.82 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" C2 LBN B 907 " pdb=" C1 LBN B 907 " pdb=" C3 LBN B 907 " pdb=" O7 LBN B 907 " both_signs ideal model delta sigma weight residual False -2.36 -2.82 0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 2969 not shown) Planarity restraints: 5556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B 749 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C TRP B 749 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP B 749 " 0.017 2.00e-02 2.50e+03 pdb=" N THR B 750 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 749 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C TRP D 749 " 0.046 2.00e-02 2.50e+03 pdb=" O TRP D 749 " -0.017 2.00e-02 2.50e+03 pdb=" N THR D 750 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 749 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C TRP A 749 " 0.046 2.00e-02 2.50e+03 pdb=" O TRP A 749 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 750 " -0.015 2.00e-02 2.50e+03 ... (remaining 5553 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 1793 2.20 - 2.80: 68064 2.80 - 3.40: 91552 3.40 - 4.00: 119500 4.00 - 4.60: 189339 Nonbonded interactions: 470248 Sorted by model distance: nonbonded pdb=" O LEU B 553 " pdb=" HG1 THR B 556 " model vdw 1.606 1.850 nonbonded pdb=" O LEU D 553 " pdb=" HG1 THR D 556 " model vdw 1.606 1.850 nonbonded pdb=" O LEU A 553 " pdb=" HG1 THR A 556 " model vdw 1.606 1.850 nonbonded pdb=" O LEU C 553 " pdb=" HG1 THR C 556 " model vdw 1.606 1.850 nonbonded pdb=" O THR D 335 " pdb=" H LEU D 339 " model vdw 1.670 1.850 ... (remaining 470243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 114 through 763) selection = (chain 'B' and resid 114 through 763) selection = (chain 'C' and resid 114 through 763) selection = (chain 'D' and resid 114 through 763) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.570 Extract box with map and model: 5.630 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 104.810 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.280 19416 Z= 0.807 Angle : 1.146 17.830 26308 Z= 0.469 Chirality : 0.060 0.460 2972 Planarity : 0.004 0.051 3224 Dihedral : 22.094 176.070 7200 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 2368 helix: 2.53 (0.14), residues: 1460 sheet: -3.29 (0.38), residues: 116 loop : -0.94 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 749 HIS 0.003 0.001 HIS C 289 PHE 0.013 0.001 PHE B 304 TYR 0.010 0.001 TYR C 584 ARG 0.008 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.640 Fit side-chains revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8599 (mtm110) cc_final: 0.8290 (mtm110) REVERT: A 710 LYS cc_start: 0.7627 (ttpp) cc_final: 0.7340 (ttmt) REVERT: B 552 MET cc_start: 0.8683 (mmm) cc_final: 0.8383 (mmm) REVERT: D 581 MET cc_start: 0.8020 (mmm) cc_final: 0.7578 (mmp) REVERT: D 760 ASN cc_start: 0.7656 (t0) cc_final: 0.7446 (t0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.7080 time to fit residues: 234.1759 Evaluate side-chains 186 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 7.9990 chunk 181 optimal weight: 40.0000 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 0.0050 chunk 122 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 217 optimal weight: 0.5980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19416 Z= 0.156 Angle : 0.483 5.217 26308 Z= 0.242 Chirality : 0.034 0.137 2972 Planarity : 0.003 0.037 3224 Dihedral : 22.274 178.915 3708 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.78 % Allowed : 4.98 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.18), residues: 2368 helix: 2.88 (0.13), residues: 1452 sheet: -3.41 (0.38), residues: 116 loop : -0.90 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 752 HIS 0.003 0.001 HIS D 289 PHE 0.017 0.001 PHE D 304 TYR 0.009 0.001 TYR A 309 ARG 0.005 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 2.722 Fit side-chains revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8604 (mtm110) cc_final: 0.8270 (mtm110) REVERT: D 581 MET cc_start: 0.8036 (mmm) cc_final: 0.7621 (mmp) outliers start: 13 outliers final: 13 residues processed: 199 average time/residue: 0.6745 time to fit residues: 203.2885 Evaluate side-chains 198 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 185 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 40.0000 chunk 218 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19416 Z= 0.421 Angle : 0.576 5.524 26308 Z= 0.298 Chirality : 0.039 0.213 2972 Planarity : 0.004 0.041 3224 Dihedral : 20.993 175.388 3708 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.62 % Allowed : 5.64 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2368 helix: 2.31 (0.14), residues: 1440 sheet: -3.39 (0.37), residues: 116 loop : -1.16 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 697 HIS 0.007 0.001 HIS D 289 PHE 0.021 0.002 PHE C 649 TYR 0.017 0.002 TYR C 530 ARG 0.005 0.001 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 2.254 Fit side-chains REVERT: C 258 THR cc_start: 0.6810 (m) cc_final: 0.6522 (m) REVERT: D 258 THR cc_start: 0.6797 (m) cc_final: 0.6571 (m) outliers start: 27 outliers final: 20 residues processed: 197 average time/residue: 0.6562 time to fit residues: 197.9708 Evaluate side-chains 198 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 19416 Z= 0.197 Angle : 0.453 4.155 26308 Z= 0.238 Chirality : 0.034 0.160 2972 Planarity : 0.003 0.045 3224 Dihedral : 19.217 173.987 3708 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.62 % Allowed : 6.29 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2368 helix: 2.56 (0.14), residues: 1460 sheet: -3.36 (0.37), residues: 116 loop : -1.14 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 697 HIS 0.003 0.001 HIS B 289 PHE 0.012 0.001 PHE D 649 TYR 0.011 0.001 TYR A 511 ARG 0.005 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 3.095 Fit side-chains REVERT: C 258 THR cc_start: 0.6840 (m) cc_final: 0.6537 (m) REVERT: D 748 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7423 (m-40) outliers start: 27 outliers final: 22 residues processed: 199 average time/residue: 0.7406 time to fit residues: 221.4026 Evaluate side-chains 202 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 118 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19416 Z= 0.327 Angle : 0.516 4.829 26308 Z= 0.270 Chirality : 0.037 0.185 2972 Planarity : 0.004 0.052 3224 Dihedral : 18.171 173.209 3708 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.74 % Allowed : 7.55 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2368 helix: 2.35 (0.14), residues: 1444 sheet: -3.37 (0.36), residues: 116 loop : -1.18 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 697 HIS 0.006 0.001 HIS A 289 PHE 0.018 0.002 PHE D 649 TYR 0.014 0.002 TYR C 530 ARG 0.004 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 2.912 Fit side-chains REVERT: C 748 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7447 (m-40) REVERT: B 748 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7431 (m-40) REVERT: D 748 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7505 (m-40) outliers start: 29 outliers final: 20 residues processed: 195 average time/residue: 0.7335 time to fit residues: 212.3232 Evaluate side-chains 199 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19416 Z= 0.286 Angle : 0.489 4.544 26308 Z= 0.258 Chirality : 0.036 0.169 2972 Planarity : 0.003 0.054 3224 Dihedral : 16.789 179.506 3708 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.62 % Allowed : 8.45 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2368 helix: 2.35 (0.14), residues: 1456 sheet: -3.34 (0.35), residues: 116 loop : -1.18 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 426 HIS 0.004 0.001 HIS B 289 PHE 0.016 0.001 PHE A 649 TYR 0.012 0.002 TYR A 511 ARG 0.006 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 2.581 Fit side-chains REVERT: A 748 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7431 (m-40) REVERT: C 748 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7455 (m-40) REVERT: B 748 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7411 (m-40) REVERT: D 748 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7439 (m-40) outliers start: 27 outliers final: 19 residues processed: 193 average time/residue: 0.7338 time to fit residues: 215.1089 Evaluate side-chains 198 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 19416 Z= 0.371 Angle : 0.542 5.104 26308 Z= 0.283 Chirality : 0.038 0.189 2972 Planarity : 0.004 0.053 3224 Dihedral : 16.317 168.802 3708 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.98 % Allowed : 8.57 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2368 helix: 2.15 (0.14), residues: 1456 sheet: -3.33 (0.35), residues: 116 loop : -1.29 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 697 HIS 0.006 0.001 HIS C 289 PHE 0.019 0.002 PHE D 649 TYR 0.015 0.002 TYR A 530 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 2.825 Fit side-chains REVERT: A 748 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7426 (m-40) REVERT: C 748 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7468 (m-40) REVERT: B 748 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7334 (m-40) REVERT: D 748 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7479 (m-40) outliers start: 33 outliers final: 22 residues processed: 200 average time/residue: 0.6925 time to fit residues: 208.3505 Evaluate side-chains 204 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 19416 Z= 0.234 Angle : 0.470 4.286 26308 Z= 0.249 Chirality : 0.035 0.164 2972 Planarity : 0.003 0.055 3224 Dihedral : 15.446 170.350 3708 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.04 % Allowed : 8.81 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2368 helix: 2.40 (0.14), residues: 1456 sheet: -3.35 (0.34), residues: 116 loop : -1.22 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 697 HIS 0.003 0.001 HIS D 289 PHE 0.013 0.001 PHE A 649 TYR 0.012 0.001 TYR A 511 ARG 0.006 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 748 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7412 (m-40) REVERT: C 748 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7454 (m-40) REVERT: B 748 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7412 (m-40) REVERT: D 748 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7415 (m-40) outliers start: 34 outliers final: 24 residues processed: 201 average time/residue: 0.6825 time to fit residues: 207.1389 Evaluate side-chains 204 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19416 Z= 0.199 Angle : 0.445 3.910 26308 Z= 0.236 Chirality : 0.034 0.151 2972 Planarity : 0.003 0.060 3224 Dihedral : 14.613 169.897 3708 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.74 % Allowed : 9.17 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.18), residues: 2368 helix: 2.61 (0.14), residues: 1456 sheet: -3.34 (0.34), residues: 116 loop : -1.13 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 697 HIS 0.003 0.001 HIS C 289 PHE 0.011 0.001 PHE B 304 TYR 0.011 0.001 TYR A 511 ARG 0.008 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 748 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7410 (m-40) REVERT: C 748 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7450 (m-40) REVERT: B 748 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7394 (m-40) REVERT: D 748 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7414 (m-40) outliers start: 29 outliers final: 25 residues processed: 196 average time/residue: 0.6941 time to fit residues: 206.3515 Evaluate side-chains 204 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 175 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 0.0070 chunk 158 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19416 Z= 0.121 Angle : 0.405 3.791 26308 Z= 0.217 Chirality : 0.033 0.129 2972 Planarity : 0.003 0.062 3224 Dihedral : 13.461 169.871 3708 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.08 % Allowed : 9.65 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.18), residues: 2368 helix: 2.96 (0.14), residues: 1456 sheet: -3.34 (0.35), residues: 116 loop : -1.08 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 697 HIS 0.005 0.001 HIS C 410 PHE 0.011 0.001 PHE B 304 TYR 0.009 0.001 TYR D 511 ARG 0.005 0.000 ARG C 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 2.534 Fit side-chains revert: symmetry clash REVERT: A 748 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7248 (m-40) REVERT: B 748 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7290 (m-40) outliers start: 18 outliers final: 16 residues processed: 198 average time/residue: 0.6792 time to fit residues: 202.9597 Evaluate side-chains 195 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 578 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.189544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136881 restraints weight = 51685.230| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.73 r_work: 0.3435 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19416 Z= 0.199 Angle : 0.438 3.865 26308 Z= 0.231 Chirality : 0.034 0.141 2972 Planarity : 0.003 0.058 3224 Dihedral : 13.521 168.714 3708 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.32 % Allowed : 9.47 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.18), residues: 2368 helix: 2.84 (0.14), residues: 1456 sheet: -3.29 (0.35), residues: 116 loop : -1.10 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 697 HIS 0.003 0.001 HIS D 410 PHE 0.012 0.001 PHE A 649 TYR 0.011 0.001 TYR D 511 ARG 0.007 0.000 ARG C 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6747.23 seconds wall clock time: 120 minutes 2.72 seconds (7202.72 seconds total)