Starting phenix.real_space_refine on Fri Mar 22 14:00:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqw_24638/03_2024/7rqw_24638_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqw_24638/03_2024/7rqw_24638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqw_24638/03_2024/7rqw_24638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqw_24638/03_2024/7rqw_24638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqw_24638/03_2024/7rqw_24638_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqw_24638/03_2024/7rqw_24638_neut_trim_updated.pdb" } resolution = 3.11 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= 0.126 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 11356 2.51 5 N 2644 2.21 5 O 3080 1.98 5 H 15804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 478": "OE1" <-> "OE2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "D GLU 478": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32984 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8070 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8070 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8070 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8070 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 218 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 218 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 134 Unusual residues: {'6EU': 1, '6OU': 2, 'PCW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 134 Unusual residues: {'6EU': 1, '6OU': 2, 'PCW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 8 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 B 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA B 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 D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 204 " occ=0.50 Time building chain proxies: 14.90, per 1000 atoms: 0.45 Number of scatterers: 32984 At special positions: 0 Unit cell: (119.88, 120.96, 109.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 12 15.00 O 3080 8.00 N 2644 7.00 C 11356 6.00 H 15804 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 B 386 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 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: 27.69 Conformation dependent library (CDL) restraints added in 3.2 seconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 8 sheets defined 57.9% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.663A pdb=" N THR A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 409 through 412 No H-bonds generated for 'chain 'A' and resid 409 through 412' Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 537 through 558 removed outlier: 3.829A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 removed outlier: 3.907A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 598 removed outlier: 4.016A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 673 through 691 removed outlier: 3.554A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 711 removed outlier: 3.585A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 719 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 223 removed outlier: 3.663A pdb=" N THR B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 409 through 412 No H-bonds generated for 'chain 'B' and resid 409 through 412' Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 537 through 558 removed outlier: 3.830A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 removed outlier: 3.907A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 598 removed outlier: 4.016A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 673 through 691 removed outlier: 3.554A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 711 removed outlier: 3.585A pdb=" N LEU B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 719 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 223 removed outlier: 3.663A pdb=" N THR C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 409 through 412 No H-bonds generated for 'chain 'C' and resid 409 through 412' Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 537 through 558 removed outlier: 3.829A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 574 removed outlier: 3.907A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 598 removed outlier: 4.015A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 673 through 691 removed outlier: 3.554A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 711 removed outlier: 3.585A pdb=" N LEU C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 719 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 223 removed outlier: 3.663A pdb=" N THR D 218 " --> pdb=" O MET D 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 221 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 409 through 412 No H-bonds generated for 'chain 'D' and resid 409 through 412' Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 537 through 558 removed outlier: 3.830A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 removed outlier: 3.906A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 598 removed outlier: 4.015A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 673 through 691 removed outlier: 3.555A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 711 removed outlier: 3.585A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 719 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 744 removed outlier: 3.645A pdb=" N TYR A 382 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.171A 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 726 Processing sheet with id= C, first strand: chain 'B' and resid 742 through 744 removed outlier: 3.645A pdb=" N TYR B 382 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 724 through 726 Processing sheet with id= E, first strand: chain 'C' and resid 742 through 744 removed outlier: 3.645A pdb=" N TYR C 382 " --> pdb=" O PHE C 742 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 724 through 726 Processing sheet with id= G, first strand: chain 'D' and resid 742 through 744 removed outlier: 3.645A pdb=" N TYR D 382 " --> pdb=" O PHE D 742 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.172A 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 726 828 hydrogen bonds defined for protein. 2436 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: 12.04 Time building geometry restraints manager: 28.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15784 1.02 - 1.22: 52 1.22 - 1.42: 7359 1.42 - 1.61: 10017 1.61 - 1.81: 180 Bond restraints: 33392 Sorted by residual: bond pdb=" CAS 6EU D 902 " pdb=" CAX 6EU D 902 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" CAS 6EU A 901 " pdb=" CAX 6EU A 901 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" CAS 6EU C 902 " pdb=" CAX 6EU C 902 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" CAS 6EU B 901 " pdb=" CAX 6EU B 901 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" CAW 6EU D 902 " pdb=" CBA 6EU D 902 " ideal model delta sigma weight residual 1.339 1.524 -0.185 2.00e-02 2.50e+03 8.52e+01 ... (remaining 33387 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.47: 270 105.47 - 112.63: 36771 112.63 - 119.78: 9372 119.78 - 126.94: 13050 126.94 - 134.10: 185 Bond angle restraints: 59648 Sorted by residual: angle pdb=" CAM 6EU A 901 " pdb=" CAV 6EU A 901 " pdb=" CBD 6EU A 901 " ideal model delta sigma weight residual 115.62 98.99 16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" CAM 6EU C 902 " pdb=" CAV 6EU C 902 " pdb=" CBD 6EU C 902 " ideal model delta sigma weight residual 115.62 98.99 16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" CAM 6EU B 901 " pdb=" CAV 6EU B 901 " pdb=" CBD 6EU B 901 " ideal model delta sigma weight residual 115.62 99.01 16.61 3.00e+00 1.11e-01 3.06e+01 angle pdb=" CAM 6EU D 902 " pdb=" CAV 6EU D 902 " pdb=" CBD 6EU D 902 " ideal model delta sigma weight residual 115.62 99.02 16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O1 LBN B 903 " pdb=" P1 LBN B 903 " pdb=" O2 LBN B 903 " ideal model delta sigma weight residual 93.45 108.96 -15.51 3.00e+00 1.11e-01 2.67e+01 ... (remaining 59643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 15816 33.92 - 67.85: 520 67.85 - 101.77: 36 101.77 - 135.70: 8 135.70 - 169.62: 8 Dihedral angle restraints: 16388 sinusoidal: 8676 harmonic: 7712 Sorted by residual: dihedral pdb=" C1 LBN A 905 " pdb=" O1 LBN A 905 " pdb=" P1 LBN A 905 " pdb=" O3 LBN A 905 " ideal model delta sinusoidal sigma weight residual 275.40 105.78 169.62 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN A 903 " pdb=" O1 LBN A 903 " pdb=" P1 LBN A 903 " pdb=" O3 LBN A 903 " ideal model delta sinusoidal sigma weight residual 275.40 105.79 169.61 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN B 906 " pdb=" O1 LBN B 906 " pdb=" P1 LBN B 906 " pdb=" O3 LBN B 906 " ideal model delta sinusoidal sigma weight residual 275.40 105.79 169.61 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 16385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2644 0.125 - 0.250: 16 0.250 - 0.375: 20 0.375 - 0.500: 4 0.500 - 0.624: 4 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CAO 6EU C 902 " pdb=" CAJ 6EU C 902 " pdb=" CAR 6EU C 902 " pdb=" CAW 6EU C 902 " both_signs ideal model delta sigma weight residual False -2.24 -2.86 0.62 2.00e-01 2.50e+01 9.75e+00 chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.86 0.62 2.00e-01 2.50e+01 9.71e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.86 0.62 2.00e-01 2.50e+01 9.66e+00 ... (remaining 2685 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 687 " 0.100 2.00e-02 2.50e+03 9.81e-02 1.44e+02 pdb=" CG ASN C 687 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 687 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN C 687 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 687 " -0.138 2.00e-02 2.50e+03 pdb="HD22 ASN C 687 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 687 " 0.100 2.00e-02 2.50e+03 9.81e-02 1.44e+02 pdb=" CG ASN B 687 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 687 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN B 687 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 687 " -0.138 2.00e-02 2.50e+03 pdb="HD22 ASN B 687 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 687 " 0.100 2.00e-02 2.50e+03 9.81e-02 1.44e+02 pdb=" CG ASN A 687 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 687 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN A 687 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 687 " -0.138 2.00e-02 2.50e+03 pdb="HD22 ASN A 687 " 0.141 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 2529 2.22 - 2.82: 68699 2.82 - 3.41: 85398 3.41 - 4.01: 112604 4.01 - 4.60: 176336 Nonbonded interactions: 445566 Sorted by model distance: nonbonded pdb=" O LEU D 506 " pdb=" HG SER D 510 " model vdw 1.625 1.850 nonbonded pdb=" O LEU C 506 " pdb=" HG SER C 510 " model vdw 1.625 1.850 nonbonded pdb=" O LEU B 506 " pdb=" HG SER B 510 " model vdw 1.625 1.850 nonbonded pdb=" O LEU A 506 " pdb=" HG SER A 510 " model vdw 1.625 1.850 nonbonded pdb=" O PHE C 369 " pdb=" H LEU C 381 " model vdw 1.632 1.850 ... (remaining 445561 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 197 through 752 or resid 904)) selection = (chain 'B' and (resid 197 through 752 or resid 904)) selection = (chain 'C' and (resid 197 through 752 or resid 904)) selection = (chain 'D' and (resid 197 through 752 or resid 904)) } 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: 1.220 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: 0.470 Extract box with map and model: 5.350 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 104.610 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 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 : 0.011 0.268 17588 Z= 0.751 Angle : 0.994 16.631 23884 Z= 0.423 Chirality : 0.056 0.624 2688 Planarity : 0.003 0.038 2928 Dihedral : 17.954 169.620 6580 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.31 (0.18), residues: 2112 helix: 0.94 (0.14), residues: 1304 sheet: -2.12 (0.55), residues: 88 loop : -0.72 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 549 HIS 0.002 0.001 HIS C 364 PHE 0.023 0.002 PHE C 659 TYR 0.016 0.002 TYR D 537 ARG 0.005 0.001 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7282 (ttpp) REVERT: A 378 HIS cc_start: 0.7408 (p90) cc_final: 0.7064 (p90) REVERT: A 445 MET cc_start: 0.7824 (mmp) cc_final: 0.7618 (mmp) REVERT: B 265 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7215 (ttpp) REVERT: B 378 HIS cc_start: 0.7417 (p90) cc_final: 0.7088 (p90) REVERT: B 445 MET cc_start: 0.7814 (mmp) cc_final: 0.7612 (mmp) REVERT: C 378 HIS cc_start: 0.7430 (p90) cc_final: 0.7141 (p90) REVERT: D 265 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7394 (ttpp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.7572 time to fit residues: 206.6096 Evaluate side-chains 151 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 160 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.6816 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17588 Z= 0.394 Angle : 0.599 4.893 23884 Z= 0.310 Chirality : 0.038 0.126 2688 Planarity : 0.003 0.028 2928 Dihedral : 16.567 169.655 3108 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.84 % Allowed : 6.04 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.10 (0.18), residues: 2112 helix: 0.76 (0.14), residues: 1300 sheet: -2.27 (0.54), residues: 88 loop : -0.78 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 549 HIS 0.003 0.001 HIS C 289 PHE 0.023 0.002 PHE D 659 TYR 0.020 0.002 TYR D 530 ARG 0.004 0.001 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7381 (ttpp) REVERT: A 378 HIS cc_start: 0.7502 (p90) cc_final: 0.7114 (p90) REVERT: B 265 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7374 (ttpp) REVERT: B 378 HIS cc_start: 0.7456 (p90) cc_final: 0.7078 (p90) REVERT: C 265 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7275 (ttpp) REVERT: C 378 HIS cc_start: 0.7474 (p90) cc_final: 0.7132 (p90) REVERT: D 265 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7404 (ttpp) outliers start: 14 outliers final: 13 residues processed: 171 average time/residue: 0.7848 time to fit residues: 190.0365 Evaluate side-chains 163 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 208 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 191 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.6797 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17588 Z= 0.283 Angle : 0.506 5.196 23884 Z= 0.267 Chirality : 0.035 0.119 2688 Planarity : 0.003 0.028 2928 Dihedral : 16.065 175.591 3108 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.84 % Allowed : 9.09 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.31 (0.18), residues: 2112 helix: 0.95 (0.14), residues: 1304 sheet: -2.33 (0.52), residues: 88 loop : -0.71 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 549 HIS 0.002 0.001 HIS C 289 PHE 0.018 0.001 PHE D 659 TYR 0.013 0.002 TYR A 530 ARG 0.003 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7382 (ttpp) REVERT: B 265 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7344 (ttpp) REVERT: B 378 HIS cc_start: 0.7568 (p90) cc_final: 0.7176 (p90) REVERT: C 265 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7213 (ttpp) REVERT: C 378 HIS cc_start: 0.7480 (p90) cc_final: 0.7118 (p90) REVERT: D 265 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7411 (ttpp) outliers start: 14 outliers final: 14 residues processed: 173 average time/residue: 0.7991 time to fit residues: 196.4510 Evaluate side-chains 161 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.9990 chunk 145 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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: 0.6743 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17588 Z= 0.161 Angle : 0.428 4.604 23884 Z= 0.227 Chirality : 0.032 0.118 2688 Planarity : 0.002 0.028 2928 Dihedral : 15.498 174.398 3108 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.02 % Allowed : 10.47 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.88 (0.18), residues: 2112 helix: 1.46 (0.15), residues: 1296 sheet: -2.22 (0.53), residues: 88 loop : -0.55 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 549 HIS 0.001 0.000 HIS C 289 PHE 0.012 0.001 PHE D 659 TYR 0.010 0.001 TYR C 309 ARG 0.001 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7379 (ttpp) REVERT: B 265 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7330 (ttpp) REVERT: B 378 HIS cc_start: 0.7585 (p90) cc_final: 0.7195 (p90) REVERT: C 378 HIS cc_start: 0.7603 (p90) cc_final: 0.7245 (p90) REVERT: D 265 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7423 (ttpp) outliers start: 17 outliers final: 16 residues processed: 180 average time/residue: 0.7834 time to fit residues: 200.5005 Evaluate side-chains 165 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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: 0.6781 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17588 Z= 0.247 Angle : 0.470 4.651 23884 Z= 0.248 Chirality : 0.034 0.118 2688 Planarity : 0.003 0.027 2928 Dihedral : 15.499 176.706 3108 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.14 % Allowed : 11.78 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.69 (0.18), residues: 2112 helix: 1.35 (0.15), residues: 1296 sheet: -2.23 (0.53), residues: 88 loop : -0.75 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 549 HIS 0.001 0.001 HIS C 289 PHE 0.016 0.001 PHE D 659 TYR 0.013 0.002 TYR C 530 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7375 (ttpp) REVERT: B 265 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7331 (ttpp) REVERT: C 378 HIS cc_start: 0.7618 (p90) cc_final: 0.7268 (p90) REVERT: D 265 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7429 (ttpp) outliers start: 19 outliers final: 18 residues processed: 177 average time/residue: 0.7769 time to fit residues: 193.8086 Evaluate side-chains 175 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.6772 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17588 Z= 0.215 Angle : 0.447 4.652 23884 Z= 0.237 Chirality : 0.033 0.119 2688 Planarity : 0.003 0.027 2928 Dihedral : 15.349 178.993 3108 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.61 % Allowed : 11.84 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.76 (0.18), residues: 2112 helix: 1.39 (0.15), residues: 1300 sheet: -2.23 (0.53), residues: 88 loop : -0.69 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 549 HIS 0.001 0.000 HIS C 378 PHE 0.014 0.001 PHE D 659 TYR 0.011 0.001 TYR B 565 ARG 0.002 0.000 ARG D 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7377 (ttpp) REVERT: B 265 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7259 (ttpp) REVERT: D 265 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7429 (ttpp) outliers start: 27 outliers final: 27 residues processed: 187 average time/residue: 0.7527 time to fit residues: 201.4776 Evaluate side-chains 184 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 204 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.6756 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17588 Z= 0.175 Angle : 0.429 5.484 23884 Z= 0.227 Chirality : 0.032 0.119 2688 Planarity : 0.002 0.027 2928 Dihedral : 15.139 179.247 3108 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.67 % Allowed : 11.90 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.89 (0.18), residues: 2112 helix: 1.54 (0.15), residues: 1296 sheet: -2.28 (0.52), residues: 88 loop : -0.73 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 549 HIS 0.001 0.000 HIS B 364 PHE 0.012 0.001 PHE C 659 TYR 0.009 0.001 TYR B 309 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7357 (ttpp) REVERT: B 265 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7257 (ttpp) REVERT: D 265 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7425 (ttpp) outliers start: 28 outliers final: 27 residues processed: 194 average time/residue: 0.7778 time to fit residues: 214.1304 Evaluate side-chains 186 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 185 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.6768 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17588 Z= 0.202 Angle : 0.440 4.632 23884 Z= 0.233 Chirality : 0.033 0.119 2688 Planarity : 0.003 0.027 2928 Dihedral : 14.984 179.861 3108 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.67 % Allowed : 12.50 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.84 (0.18), residues: 2112 helix: 1.47 (0.15), residues: 1300 sheet: -2.29 (0.53), residues: 88 loop : -0.69 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 549 HIS 0.001 0.000 HIS C 289 PHE 0.012 0.001 PHE D 659 TYR 0.010 0.001 TYR C 530 ARG 0.002 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7357 (ttpp) REVERT: B 265 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7258 (ttpp) REVERT: D 265 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7413 (ttpp) outliers start: 28 outliers final: 28 residues processed: 188 average time/residue: 0.7946 time to fit residues: 213.3169 Evaluate side-chains 188 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 82 optimal weight: 0.1980 chunk 149 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 189 optimal weight: 0.2980 chunk 125 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.6719 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17588 Z= 0.127 Angle : 0.402 7.612 23884 Z= 0.212 Chirality : 0.031 0.120 2688 Planarity : 0.002 0.026 2928 Dihedral : 14.247 175.298 3108 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.26 % Allowed : 12.98 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.20 (0.19), residues: 2112 helix: 1.80 (0.15), residues: 1300 sheet: -2.41 (0.53), residues: 88 loop : -0.59 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP D 549 HIS 0.001 0.000 HIS D 364 PHE 0.010 0.001 PHE B 489 TYR 0.009 0.001 TYR B 309 ARG 0.001 0.000 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7353 (ttpp) REVERT: A 308 MET cc_start: 0.8591 (tmm) cc_final: 0.8390 (tmm) REVERT: B 265 LYS cc_start: 0.7829 (ttmt) cc_final: 0.7252 (ttpp) REVERT: B 378 HIS cc_start: 0.7524 (p90) cc_final: 0.7259 (p90) REVERT: C 309 TYR cc_start: 0.6877 (t80) cc_final: 0.6609 (t80) REVERT: D 265 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7389 (ttpp) outliers start: 21 outliers final: 20 residues processed: 186 average time/residue: 0.8290 time to fit residues: 214.4376 Evaluate side-chains 184 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 139 optimal weight: 0.0870 chunk 211 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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: 0.6741 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17588 Z= 0.158 Angle : 0.412 4.925 23884 Z= 0.218 Chirality : 0.032 0.119 2688 Planarity : 0.002 0.026 2928 Dihedral : 14.172 173.591 3108 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.20 % Allowed : 13.28 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.19 (0.19), residues: 2112 helix: 1.79 (0.15), residues: 1300 sheet: -2.35 (0.54), residues: 88 loop : -0.60 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 549 HIS 0.001 0.000 HIS A 289 PHE 0.010 0.001 PHE D 489 TYR 0.008 0.001 TYR B 309 ARG 0.001 0.000 ARG D 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 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 LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7308 (ttpp) REVERT: B 265 LYS cc_start: 0.7834 (ttmt) cc_final: 0.7255 (ttpp) REVERT: B 378 HIS cc_start: 0.7496 (p90) cc_final: 0.7240 (p90) REVERT: C 309 TYR cc_start: 0.6931 (t80) cc_final: 0.6667 (t80) REVERT: C 378 HIS cc_start: 0.7587 (p90) cc_final: 0.7316 (p90) REVERT: D 265 LYS cc_start: 0.7849 (ttmt) cc_final: 0.7390 (ttpp) outliers start: 20 outliers final: 20 residues processed: 182 average time/residue: 0.8991 time to fit residues: 228.2308 Evaluate side-chains 179 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4549 r_free = 0.4549 target = 0.237805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.186888 restraints weight = 47696.511| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.85 r_work: 0.3564 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17588 Z= 0.196 Angle : 0.434 4.617 23884 Z= 0.229 Chirality : 0.032 0.117 2688 Planarity : 0.003 0.026 2928 Dihedral : 14.313 175.421 3108 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.50 % Allowed : 13.16 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.03 (0.18), residues: 2112 helix: 1.66 (0.15), residues: 1300 sheet: -2.38 (0.53), residues: 88 loop : -0.66 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 549 HIS 0.002 0.000 HIS A 358 PHE 0.011 0.001 PHE A 659 TYR 0.010 0.001 TYR C 530 ARG 0.002 0.000 ARG D 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6234.89 seconds wall clock time: 111 minutes 8.93 seconds (6668.93 seconds total)