Starting phenix.real_space_refine on Thu Feb 22 18:00:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqv_24637/02_2024/7rqv_24637_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqv_24637/02_2024/7rqv_24637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqv_24637/02_2024/7rqv_24637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqv_24637/02_2024/7rqv_24637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqv_24637/02_2024/7rqv_24637_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqv_24637/02_2024/7rqv_24637_trim_updated.pdb" } resolution = 3.45 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 92 5.16 5 Na 2 4.78 5 C 11856 2.51 5 N 2880 2.21 5 O 3220 1.98 5 H 16236 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34298 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 8417 Classifications: {'peptide': 580} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 565} Chain breaks: 5 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 177 Chain: "C" Number of atoms: 8417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 8417 Classifications: {'peptide': 580} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 565} Chain breaks: 5 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 177 Chain: "D" Number of atoms: 8417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 8417 Classifications: {'peptide': 580} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 565} Chain breaks: 5 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 177 Chain: "B" Number of atoms: 8417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 8417 Classifications: {'peptide': 580} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 565} Chain breaks: 5 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 177 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 192 Unusual residues: {' NA': 2, '6EU': 1, '6OU': 4, 'LBN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 157 Unusual residues: {'6EU': 1, '6OU': 3, 'LBN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 157 Unusual residues: {'6EU': 1, '6OU': 3, 'LBN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 13 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA A 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 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 Time building chain proxies: 16.10, per 1000 atoms: 0.47 Number of scatterers: 34298 At special positions: 0 Unit cell: (124.2, 124.2, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 92 16.00 P 12 15.00 Na 2 11.00 O 3220 8.00 N 2880 7.00 C 11856 6.00 H 16236 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=2.53 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.53 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.53 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.53 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.72 Conformation dependent library (CDL) restraints added in 4.0 seconds 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 8 sheets defined 53.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.69 Creating SS restraints... Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 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 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 416 through 429 removed outlier: 4.278A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 452 removed outlier: 3.730A pdb=" N ILE A 446 " --> pdb=" O CYS A 442 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 449 " --> pdb=" O MET A 445 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 499 removed outlier: 3.897A pdb=" N TYR A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 498 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 removed outlier: 5.384A pdb=" N PHE A 507 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 508 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 509 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 removed outlier: 3.513A pdb=" N MET A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 555 removed outlier: 3.830A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 563 No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 568 through 575 removed outlier: 3.932A pdb=" N ILE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 656 through 670 removed outlier: 3.661A pdb=" N ILE A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 removed outlier: 4.252A pdb=" N ALA A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 711 removed outlier: 3.735A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 716 No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 204 through 211 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 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 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 416 through 429 removed outlier: 4.278A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 452 removed outlier: 3.730A pdb=" N ILE C 446 " --> pdb=" O CYS C 442 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 449 " --> pdb=" O MET C 445 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 450 " --> pdb=" O ILE C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 499 removed outlier: 3.897A pdb=" N TYR C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 496 " --> pdb=" O GLY C 492 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 509 removed outlier: 5.384A pdb=" N PHE C 507 " --> pdb=" O LYS C 504 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C 508 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP C 509 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 531 removed outlier: 3.513A pdb=" N MET C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 555 removed outlier: 3.830A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 563 No H-bonds generated for 'chain 'C' and resid 560 through 563' Processing helix chain 'C' and resid 568 through 575 removed outlier: 3.932A pdb=" N ILE C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 582 No H-bonds generated for 'chain 'C' and resid 579 through 582' Processing helix chain 'C' and resid 585 through 598 Processing helix chain 'C' and resid 630 through 636 Processing helix chain 'C' and resid 656 through 670 removed outlier: 3.661A pdb=" N ILE C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 664 " --> pdb=" O ILE C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 691 removed outlier: 4.252A pdb=" N ALA C 680 " --> pdb=" O ASN C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 711 removed outlier: 3.735A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 716 No H-bonds generated for 'chain 'C' and resid 713 through 716' Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 204 through 211 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 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 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 416 through 429 removed outlier: 4.278A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 452 removed outlier: 3.730A pdb=" N ILE D 446 " --> pdb=" O CYS D 442 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR D 449 " --> pdb=" O MET D 445 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 499 removed outlier: 3.897A pdb=" N TYR D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE D 496 " --> pdb=" O GLY D 492 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN D 498 " --> pdb=" O GLN D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 509 removed outlier: 5.384A pdb=" N PHE D 507 " --> pdb=" O LYS D 504 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL D 508 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP D 509 " --> pdb=" O LEU D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 removed outlier: 3.512A pdb=" N MET D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 555 removed outlier: 3.831A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 563 No H-bonds generated for 'chain 'D' and resid 560 through 563' Processing helix chain 'D' and resid 568 through 575 removed outlier: 3.933A pdb=" N ILE D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 582 No H-bonds generated for 'chain 'D' and resid 579 through 582' Processing helix chain 'D' and resid 585 through 598 Processing helix chain 'D' and resid 630 through 636 Processing helix chain 'D' and resid 656 through 670 removed outlier: 3.661A pdb=" N ILE D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 664 " --> pdb=" O ILE D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 691 removed outlier: 4.251A pdb=" N ALA D 680 " --> pdb=" O ASN D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 711 removed outlier: 3.735A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 716 No H-bonds generated for 'chain 'D' and resid 713 through 716' Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 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 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 416 through 429 removed outlier: 4.277A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 452 removed outlier: 3.730A pdb=" N ILE B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 449 " --> pdb=" O MET B 445 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 499 removed outlier: 3.897A pdb=" N TYR B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 496 " --> pdb=" O GLY B 492 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN B 498 " --> pdb=" O GLN B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 removed outlier: 5.383A pdb=" N PHE B 507 " --> pdb=" O LYS B 504 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 508 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 509 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 removed outlier: 3.513A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 555 removed outlier: 3.830A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 563 No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing helix chain 'B' and resid 568 through 575 removed outlier: 3.931A pdb=" N ILE B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 582 No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 585 through 598 Processing helix chain 'B' and resid 630 through 636 Processing helix chain 'B' and resid 656 through 670 removed outlier: 3.660A pdb=" N ILE B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 691 removed outlier: 4.252A pdb=" N ALA B 680 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 711 removed outlier: 3.735A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 716 No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing sheet with id= A, first strand: chain 'A' and resid 377 through 380 Processing sheet with id= B, first strand: chain 'A' and resid 724 through 730 removed outlier: 7.105A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 377 through 380 Processing sheet with id= D, first strand: chain 'C' and resid 724 through 730 removed outlier: 7.105A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 377 through 380 Processing sheet with id= F, first strand: chain 'D' and resid 724 through 730 removed outlier: 7.105A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 377 through 380 Processing sheet with id= H, first strand: chain 'B' and resid 724 through 730 removed outlier: 7.105A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2196 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: 12.27 Time building geometry restraints manager: 27.47 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: 16208 1.02 - 1.21: 80 1.21 - 1.41: 7700 1.41 - 1.61: 10512 1.61 - 1.81: 192 Bond restraints: 34692 Sorted by residual: bond pdb=" CAS 6EU D 904 " pdb=" CAX 6EU D 904 " ideal model delta sigma weight residual 1.334 1.608 -0.274 2.00e-02 2.50e+03 1.87e+02 bond pdb=" CAS 6EU A 905 " pdb=" CAX 6EU A 905 " ideal model delta sigma weight residual 1.334 1.608 -0.274 2.00e-02 2.50e+03 1.87e+02 bond pdb=" CAS 6EU C 905 " pdb=" CAX 6EU C 905 " ideal model delta sigma weight residual 1.334 1.607 -0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" CAS 6EU B 905 " pdb=" CAX 6EU B 905 " ideal model delta sigma weight residual 1.334 1.607 -0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" CAW 6EU A 905 " pdb=" CBA 6EU A 905 " ideal model delta sigma weight residual 1.339 1.521 -0.182 2.00e-02 2.50e+03 8.27e+01 ... (remaining 34687 not shown) Histogram of bond angle deviations from ideal: 79.85 - 90.68: 16 90.68 - 101.52: 60 101.52 - 112.35: 37526 112.35 - 123.19: 21125 123.19 - 134.03: 3121 Bond angle restraints: 61848 Sorted by residual: angle pdb="HD11 ILE A 679 " pdb=" CD1 ILE A 679 " pdb="HD12 ILE A 679 " ideal model delta sigma weight residual 110.00 80.71 29.29 3.00e+00 1.11e-01 9.53e+01 angle pdb="HD11 ILE B 679 " pdb=" CD1 ILE B 679 " pdb="HD12 ILE B 679 " ideal model delta sigma weight residual 110.00 80.73 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb="HD11 ILE D 679 " pdb=" CD1 ILE D 679 " pdb="HD12 ILE D 679 " ideal model delta sigma weight residual 110.00 80.73 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb="HD11 ILE C 679 " pdb=" CD1 ILE C 679 " pdb="HD12 ILE C 679 " ideal model delta sigma weight residual 110.00 80.74 29.26 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CG1 ILE A 679 " pdb=" CD1 ILE A 679 " pdb="HD11 ILE A 679 " ideal model delta sigma weight residual 109.00 79.85 29.15 3.00e+00 1.11e-01 9.44e+01 ... (remaining 61843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 16584 35.85 - 71.70: 468 71.70 - 107.55: 36 107.55 - 143.40: 20 143.40 - 179.25: 4 Dihedral angle restraints: 17112 sinusoidal: 8812 harmonic: 8300 Sorted by residual: dihedral pdb=" CB CYS D 386 " pdb=" SG CYS D 386 " pdb=" SG CYS D 390 " pdb=" CB CYS D 390 " ideal model delta sinusoidal sigma weight residual 93.00 19.55 73.45 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS B 386 " pdb=" SG CYS B 386 " pdb=" SG CYS B 390 " pdb=" CB CYS B 390 " ideal model delta sinusoidal sigma weight residual 93.00 19.57 73.43 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS C 386 " pdb=" SG CYS C 386 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual 93.00 19.57 73.43 1 1.00e+01 1.00e-02 6.86e+01 ... (remaining 17109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2743 0.094 - 0.188: 69 0.188 - 0.281: 12 0.281 - 0.375: 12 0.375 - 0.469: 16 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CAO 6EU B 905 " pdb=" CAJ 6EU B 905 " pdb=" CAR 6EU B 905 " pdb=" CAW 6EU B 905 " both_signs ideal model delta sigma weight residual False -2.24 -2.70 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CAO 6EU C 905 " pdb=" CAJ 6EU C 905 " pdb=" CAR 6EU C 905 " pdb=" CAW 6EU C 905 " both_signs ideal model delta sigma weight residual False -2.24 -2.70 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CAO 6EU D 904 " pdb=" CAJ 6EU D 904 " pdb=" CAR 6EU D 904 " pdb=" CAW 6EU D 904 " both_signs ideal model delta sigma weight residual False -2.24 -2.70 0.47 2.00e-01 2.50e+01 5.44e+00 ... (remaining 2849 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 691 " 0.028 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" N GLU C 692 " -0.093 2.00e-02 2.50e+03 pdb=" CA GLU C 692 " 0.023 2.00e-02 2.50e+03 pdb=" H GLU C 692 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 691 " -0.028 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" N GLU A 692 " 0.093 2.00e-02 2.50e+03 pdb=" CA GLU A 692 " -0.023 2.00e-02 2.50e+03 pdb=" H GLU A 692 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 691 " 0.028 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" N GLU B 692 " -0.093 2.00e-02 2.50e+03 pdb=" CA GLU B 692 " 0.023 2.00e-02 2.50e+03 pdb=" H GLU B 692 " 0.042 2.00e-02 2.50e+03 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1879 2.20 - 2.80: 66695 2.80 - 3.40: 87721 3.40 - 4.00: 113890 4.00 - 4.60: 177687 Nonbonded interactions: 447872 Sorted by model distance: nonbonded pdb=" O THR A 298 " pdb=" H THR A 302 " model vdw 1.598 1.850 nonbonded pdb=" O THR C 298 " pdb=" H THR C 302 " model vdw 1.599 1.850 nonbonded pdb=" O THR B 298 " pdb=" H THR B 302 " model vdw 1.599 1.850 nonbonded pdb=" O THR D 298 " pdb=" H THR D 302 " model vdw 1.600 1.850 nonbonded pdb=" O PHE B 496 " pdb=" H ARG B 500 " model vdw 1.608 1.850 ... (remaining 447867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 114 through 752 or resid 901 through 902)) selection = (chain 'B' and (resid 114 through 752 or resid 901 through 902)) selection = (chain 'C' and (resid 114 through 752 or resid 901 through 902)) selection = (chain 'D' and (resid 114 through 752 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.540 Extract box with map and model: 5.630 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 108.490 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 0.274 18456 Z= 0.697 Angle : 0.974 14.832 25060 Z= 0.466 Chirality : 0.055 0.469 2852 Planarity : 0.005 0.088 3092 Dihedral : 18.054 179.246 6704 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.71 (0.18), residues: 2272 helix: 0.03 (0.15), residues: 1344 sheet: -4.03 (0.34), residues: 68 loop : -0.78 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 697 HIS 0.003 0.001 HIS C 410 PHE 0.013 0.001 PHE C 448 TYR 0.014 0.001 TYR B 444 ARG 0.007 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.573 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 outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.5615 time to fit residues: 215.7844 Evaluate side-chains 192 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 118 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 210 optimal weight: 0.5980 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: 0.7272 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18456 Z= 0.150 Angle : 0.494 5.520 25060 Z= 0.267 Chirality : 0.034 0.130 2852 Planarity : 0.004 0.078 3092 Dihedral : 15.872 179.245 3244 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.85 % Allowed : 6.82 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.18 (0.18), residues: 2272 helix: 0.55 (0.15), residues: 1348 sheet: -3.74 (0.38), residues: 68 loop : -0.76 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 697 HIS 0.002 0.001 HIS C 364 PHE 0.012 0.001 PHE C 304 TYR 0.009 0.001 TYR B 444 ARG 0.004 0.000 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 346 ILE cc_start: 0.8682 (tt) cc_final: 0.8459 (tt) REVERT: B 656 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7755 (ttpt) outliers start: 14 outliers final: 12 residues processed: 214 average time/residue: 0.5948 time to fit residues: 198.1564 Evaluate side-chains 198 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 chunk 175 optimal weight: 30.0000 chunk 143 optimal weight: 4.9990 chunk 58 optimal weight: 40.0000 chunk 211 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 209 optimal weight: 0.0060 chunk 71 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18456 Z= 0.275 Angle : 0.524 5.882 25060 Z= 0.283 Chirality : 0.036 0.131 2852 Planarity : 0.004 0.062 3092 Dihedral : 14.816 170.021 3244 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.91 % Allowed : 7.55 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.28 (0.18), residues: 2272 helix: 0.50 (0.15), residues: 1348 sheet: -3.86 (0.37), residues: 68 loop : -0.84 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 426 HIS 0.002 0.001 HIS A 358 PHE 0.017 0.001 PHE B 587 TYR 0.013 0.001 TYR A 444 ARG 0.005 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 LEU cc_start: 0.7792 (tp) cc_final: 0.7555 (tp) REVERT: B 656 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7794 (ttpt) outliers start: 15 outliers final: 14 residues processed: 213 average time/residue: 0.5756 time to fit residues: 193.9492 Evaluate side-chains 203 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 189 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 60 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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: 0.7299 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18456 Z= 0.135 Angle : 0.440 4.385 25060 Z= 0.238 Chirality : 0.032 0.123 2852 Planarity : 0.003 0.057 3092 Dihedral : 13.312 168.437 3244 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.72 % Allowed : 7.61 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.22 (0.19), residues: 2272 helix: 0.92 (0.15), residues: 1348 sheet: -3.50 (0.42), residues: 68 loop : -0.68 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 426 HIS 0.002 0.001 HIS B 364 PHE 0.013 0.001 PHE A 429 TYR 0.015 0.001 TYR D 309 ARG 0.002 0.000 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 2.741 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: B 656 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7780 (ttpt) outliers start: 12 outliers final: 11 residues processed: 223 average time/residue: 0.5547 time to fit residues: 195.8331 Evaluate side-chains 212 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 114 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7401 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18456 Z= 0.322 Angle : 0.531 5.717 25060 Z= 0.286 Chirality : 0.037 0.129 2852 Planarity : 0.004 0.050 3092 Dihedral : 14.090 168.430 3244 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.72 % Allowed : 8.45 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.22 (0.18), residues: 2272 helix: 0.60 (0.15), residues: 1344 sheet: -3.90 (0.39), residues: 68 loop : -0.92 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 426 HIS 0.003 0.001 HIS B 358 PHE 0.017 0.002 PHE B 448 TYR 0.014 0.002 TYR D 309 ARG 0.004 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 325 LEU cc_start: 0.7823 (tp) cc_final: 0.7603 (mm) REVERT: B 656 LYS cc_start: 0.8011 (ttpt) cc_final: 0.7784 (ttpt) outliers start: 12 outliers final: 12 residues processed: 203 average time/residue: 0.5796 time to fit residues: 186.0940 Evaluate side-chains 200 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 687 ASN D 687 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18456 Z= 0.312 Angle : 0.529 5.611 25060 Z= 0.287 Chirality : 0.036 0.129 2852 Planarity : 0.004 0.052 3092 Dihedral : 14.109 168.273 3244 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.97 % Allowed : 9.36 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.51 (0.18), residues: 2272 helix: 0.37 (0.15), residues: 1344 sheet: -4.05 (0.39), residues: 68 loop : -1.04 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 426 HIS 0.003 0.001 HIS C 358 PHE 0.016 0.002 PHE C 649 TYR 0.013 0.002 TYR D 309 ARG 0.002 0.000 ARG C 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 325 LEU cc_start: 0.7860 (tp) cc_final: 0.7632 (mm) outliers start: 16 outliers final: 16 residues processed: 216 average time/residue: 0.6032 time to fit residues: 208.1909 Evaluate side-chains 210 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 138 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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: 0.7401 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18456 Z= 0.236 Angle : 0.488 4.957 25060 Z= 0.266 Chirality : 0.034 0.128 2852 Planarity : 0.003 0.043 3092 Dihedral : 13.679 167.570 3244 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.91 % Allowed : 10.39 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.32 (0.18), residues: 2272 helix: 0.55 (0.15), residues: 1344 sheet: -4.07 (0.38), residues: 68 loop : -0.98 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 697 HIS 0.002 0.001 HIS C 364 PHE 0.013 0.001 PHE C 649 TYR 0.016 0.001 TYR A 309 ARG 0.004 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7336 (tt) REVERT: B 325 LEU cc_start: 0.7846 (tp) cc_final: 0.7636 (mm) outliers start: 15 outliers final: 14 residues processed: 212 average time/residue: 0.5664 time to fit residues: 190.6367 Evaluate side-chains 205 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7365 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18456 Z= 0.157 Angle : 0.449 4.602 25060 Z= 0.245 Chirality : 0.033 0.126 2852 Planarity : 0.003 0.044 3092 Dihedral : 12.822 167.005 3244 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.03 % Allowed : 10.39 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.05 (0.18), residues: 2272 helix: 0.79 (0.15), residues: 1344 sheet: -3.96 (0.40), residues: 68 loop : -0.92 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 697 HIS 0.002 0.001 HIS C 364 PHE 0.012 0.001 PHE A 429 TYR 0.015 0.001 TYR A 309 ARG 0.002 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7099 (tt) REVERT: A 325 LEU cc_start: 0.7962 (tp) cc_final: 0.7750 (mm) REVERT: B 261 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7249 (tt) REVERT: B 325 LEU cc_start: 0.7834 (tp) cc_final: 0.7634 (mm) outliers start: 17 outliers final: 14 residues processed: 214 average time/residue: 0.5955 time to fit residues: 203.5778 Evaluate side-chains 209 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 136 optimal weight: 0.0570 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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: 0.7401 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18456 Z= 0.256 Angle : 0.488 5.079 25060 Z= 0.264 Chirality : 0.035 0.128 2852 Planarity : 0.003 0.040 3092 Dihedral : 12.942 166.634 3244 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.97 % Allowed : 10.99 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.17 (0.18), residues: 2272 helix: 0.69 (0.15), residues: 1344 sheet: -4.12 (0.39), residues: 68 loop : -0.96 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 426 HIS 0.002 0.001 HIS B 358 PHE 0.019 0.001 PHE A 429 TYR 0.016 0.001 TYR A 309 ARG 0.003 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7225 (tt) REVERT: B 261 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7327 (tt) REVERT: B 325 LEU cc_start: 0.7834 (tp) cc_final: 0.7627 (mm) outliers start: 16 outliers final: 14 residues processed: 214 average time/residue: 0.5686 time to fit residues: 192.6245 Evaluate side-chains 210 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.7385 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18456 Z= 0.204 Angle : 0.465 4.877 25060 Z= 0.253 Chirality : 0.034 0.127 2852 Planarity : 0.003 0.041 3092 Dihedral : 12.495 166.081 3244 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.97 % Allowed : 11.35 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.08 (0.18), residues: 2272 helix: 0.77 (0.15), residues: 1344 sheet: -4.04 (0.40), residues: 68 loop : -0.95 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 697 HIS 0.002 0.001 HIS A 364 PHE 0.018 0.001 PHE A 429 TYR 0.015 0.001 TYR A 309 ARG 0.002 0.000 ARG C 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7141 (tt) REVERT: B 261 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7267 (tt) outliers start: 16 outliers final: 14 residues processed: 209 average time/residue: 0.5653 time to fit residues: 187.4238 Evaluate side-chains 209 residues out of total 2048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.186973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.157295 restraints weight = 58406.602| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.32 r_work: 0.3698 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18456 Z= 0.311 Angle : 0.526 6.975 25060 Z= 0.283 Chirality : 0.036 0.130 2852 Planarity : 0.004 0.040 3092 Dihedral : 12.933 165.855 3244 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.97 % Allowed : 11.41 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.34 (0.18), residues: 2272 helix: 0.56 (0.15), residues: 1344 sheet: -4.23 (0.39), residues: 68 loop : -1.04 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 426 HIS 0.003 0.001 HIS B 358 PHE 0.019 0.002 PHE A 429 TYR 0.015 0.002 TYR A 309 ARG 0.004 0.000 ARG A 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6196.15 seconds wall clock time: 110 minutes 49.12 seconds (6649.12 seconds total)