Starting phenix.real_space_refine on Fri Mar 22 23:41:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uow_8579/03_2024/5uow_8579_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uow_8579/03_2024/5uow_8579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uow_8579/03_2024/5uow_8579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uow_8579/03_2024/5uow_8579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uow_8579/03_2024/5uow_8579_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uow_8579/03_2024/5uow_8579_neut_updated.pdb" } resolution = 4.5 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10586 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 15525 2.51 5 N 4158 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A GLU 785": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ARG 680": "NH1" <-> "NH2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "B GLU 1101": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24347 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 5758 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 35, 'TRANS': 761} Chain breaks: 1 Unresolved non-hydrogen bonds: 565 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 15, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 25, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 367 Chain: "B" Number of atoms: 5582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5582 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PTRANS': 28, 'TRANS': 766} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 937 Unresolved non-hydrogen dihedrals: 625 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 18, 'ASP:plan': 21, 'PHE:plan': 14, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 453 Chain: "C" Number of atoms: 5484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 5484 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 762} Chain breaks: 1 Unresolved non-hydrogen bonds: 872 Unresolved non-hydrogen angles: 1095 Unresolved non-hydrogen dihedrals: 735 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 15, 'TRP:plan': 6, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 556 Chain: "D" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5127 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 327} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 765} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1224 Unresolved non-hydrogen angles: 1520 Unresolved non-hydrogen dihedrals: 1021 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 18, 'TRP:plan': 2, 'ASP:plan': 30, 'PHE:plan': 17, 'GLU:plan': 42, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 731 Chain: "F" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1070 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'CIS': 3, 'TRANS': 210} Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 642 Unresolved non-hydrogen dihedrals: 214 Planarities with less than four sites: {'UNK:plan-1': 214} Unresolved non-hydrogen planarities: 214 Chain: "G" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1075 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'CIS': 3, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 215 Planarities with less than four sites: {'UNK:plan-1': 215} Unresolved non-hydrogen planarities: 215 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'BMK': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Time building chain proxies: 13.24, per 1000 atoms: 0.54 Number of scatterers: 24347 At special positions: 0 Unit cell: (197.2, 113.9, 185.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4554 8.00 N 4158 7.00 C 15525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 452 " distance=2.06 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 453 " distance=2.03 Simple disulfide: pdb=" SG CYS A 742 " - pdb=" SG CYS A 796 " distance=2.08 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 312 " distance=2.01 Simple disulfide: pdb=" SG CYS B 417 " - pdb=" SG CYS B 443 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 444 " distance=2.02 Simple disulfide: pdb=" SG CYS B 733 " - pdb=" SG CYS B 788 " distance=2.08 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.05 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 452 " distance=2.04 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 453 " distance=2.04 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 796 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 316 " distance=2.04 Simple disulfide: pdb=" SG CYS D 422 " - pdb=" SG CYS D 449 " distance=2.02 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 450 " distance=2.03 Simple disulfide: pdb=" SG CYS D 739 " - pdb=" SG CYS D 794 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG E 1 " - " ASN A 61 " " NAG H 1 " - " ASN A 203 " " NAG I 1 " - " ASN A 276 " " NAG J 1 " - " ASN C 61 " " NAG K 1 " - " ASN C 203 " " NAG L 1 " - " ASN C 276 " " NAG M 1 " - " ASN D 336 " " NAG N 1 " - " ASN D 681 " Time building additional restraints: 10.30 Conformation dependent library (CDL) restraints added in 4.4 seconds 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6834 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 40 sheets defined 41.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'A' and resid 36 through 52 removed outlier: 4.364A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 103 through 114 Proline residue: A 106 - end of helix removed outlier: 4.155A pdb=" N ALA A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.659A pdb=" N PHE A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 158 " --> pdb=" O MET A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.790A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.516A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.608A pdb=" N ALA A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 277 through 297 removed outlier: 3.859A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 456 through 467 Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 519 through 522 No H-bonds generated for 'chain 'A' and resid 519 through 522' Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.618A pdb=" N GLN A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Proline residue: A 555 - end of helix Processing helix chain 'A' and resid 560 through 579 removed outlier: 3.727A pdb=" N GLY A 565 " --> pdb=" O TRP A 561 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 573 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 625 through 654 removed outlier: 4.163A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 671 No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 686 through 693 removed outlier: 3.502A pdb=" N TYR A 690 " --> pdb=" O SER A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 707 removed outlier: 5.101A pdb=" N THR A 699 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 702 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 706 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 3.869A pdb=" N VAL A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 741 removed outlier: 4.256A pdb=" N PHE A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 779 Processing helix chain 'A' and resid 782 through 793 removed outlier: 4.398A pdb=" N TYR A 793 " --> pdb=" O THR A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 834 removed outlier: 3.530A pdb=" N ASN A 810 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 829 " --> pdb=" O ILE A 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 removed outlier: 4.404A pdb=" N LEU B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASP B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 84 removed outlier: 3.717A pdb=" N GLY B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 121 through 124 No H-bonds generated for 'chain 'B' and resid 121 through 124' Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.520A pdb=" N ILE B 176 " --> pdb=" O TYR B 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.508A pdb=" N LYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 238 removed outlier: 3.575A pdb=" N SER B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 254 No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 280 through 298 removed outlier: 4.065A pdb=" N VAL B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 533 through 567 removed outlier: 3.876A pdb=" N LEU B 538 " --> pdb=" O PRO B 534 " (cutoff:3.500A) Proline residue: B 540 - end of helix removed outlier: 4.052A pdb=" N SER B 544 " --> pdb=" O PRO B 540 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 566 " --> pdb=" O PHE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 600 removed outlier: 3.803A pdb=" N ILE B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP B 597 " --> pdb=" O TRP B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 643 removed outlier: 3.780A pdb=" N ILE B 617 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 659 No H-bonds generated for 'chain 'B' and resid 656 through 659' Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'B' and resid 677 through 683 removed outlier: 3.694A pdb=" N ASN B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 720 through 729 Processing helix chain 'B' and resid 759 through 772 removed outlier: 3.920A pdb=" N LEU B 765 " --> pdb=" O ARG B 761 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 766 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 802 through 827 Processing helix chain 'C' and resid 36 through 52 Processing helix chain 'C' and resid 71 through 79 removed outlier: 4.143A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 Proline residue: C 106 - end of helix removed outlier: 4.154A pdb=" N ALA C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.531A pdb=" N LEU C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 removed outlier: 3.826A pdb=" N GLU C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 237 removed outlier: 4.162A pdb=" N THR C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 237 " --> pdb=" O LYS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 277 through 295 removed outlier: 3.522A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 456 through 467 Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 498 through 505 removed outlier: 3.777A pdb=" N GLU C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 503 " --> pdb=" O MET C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 522 No H-bonds generated for 'chain 'C' and resid 519 through 522' Processing helix chain 'C' and resid 549 through 581 Proline residue: C 555 - end of helix removed outlier: 4.643A pdb=" N SER C 558 " --> pdb=" O GLN C 554 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR C 559 " --> pdb=" O PRO C 555 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 560 " --> pdb=" O PHE C 556 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS C 569 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 576 " --> pdb=" O ALA C 572 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 613 removed outlier: 4.059A pdb=" N VAL C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 612 " --> pdb=" O SER C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 654 removed outlier: 3.561A pdb=" N LEU C 636 " --> pdb=" O MET C 632 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL C 654 " --> pdb=" O ALA C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 671 No H-bonds generated for 'chain 'C' and resid 668 through 671' Processing helix chain 'C' and resid 686 through 693 Processing helix chain 'C' and resid 699 through 706 removed outlier: 4.032A pdb=" N LYS C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 720 Processing helix chain 'C' and resid 731 through 740 removed outlier: 3.825A pdb=" N PHE C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 780 Processing helix chain 'C' and resid 782 through 791 Processing helix chain 'C' and resid 805 through 835 removed outlier: 4.367A pdb=" N ASN C 810 " --> pdb=" O LEU C 806 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET C 811 " --> pdb=" O THR C 807 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 813 " --> pdb=" O GLU C 809 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 819 " --> pdb=" O PHE C 815 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 822 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA C 824 " --> pdb=" O GLY C 820 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 827 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.767A pdb=" N PHE D 54 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.805A pdb=" N CYS D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP D 86 " --> pdb=" O ASP D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 123 through 126 No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'D' and resid 145 through 158 Processing helix chain 'D' and resid 174 through 187 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 229 through 242 Processing helix chain 'D' and resid 255 through 258 No H-bonds generated for 'chain 'D' and resid 255 through 258' Processing helix chain 'D' and resid 284 through 306 removed outlier: 3.929A pdb=" N HIS D 306 " --> pdb=" O MET D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 335 Processing helix chain 'D' and resid 453 through 465 removed outlier: 3.618A pdb=" N THR D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 495 Processing helix chain 'D' and resid 510 through 515 Processing helix chain 'D' and resid 544 through 548 Processing helix chain 'D' and resid 550 through 573 Processing helix chain 'D' and resid 596 through 606 Processing helix chain 'D' and resid 620 through 648 Processing helix chain 'D' and resid 683 through 691 Processing helix chain 'D' and resid 693 through 701 removed outlier: 5.193A pdb=" N LYS D 701 " --> pdb=" O SER D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 715 Processing helix chain 'D' and resid 726 through 734 Processing helix chain 'D' and resid 766 through 779 removed outlier: 3.531A pdb=" N ALA D 772 " --> pdb=" O GLN D 768 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 773 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 777 " --> pdb=" O ILE D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 789 Processing helix chain 'D' and resid 810 through 836 removed outlier: 3.647A pdb=" N TYR D 836 " --> pdb=" O GLU D 832 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 62 through 65 No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing sheet with id= A, first strand: chain 'A' and resid 59 through 65 removed outlier: 4.711A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL A 92 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 119 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 194 through 197 removed outlier: 6.283A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL A 246 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 221 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 248 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 268 through 271 Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.685A pdb=" N ASP A 368 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.808A pdb=" N THR A 471 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE A 400 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 473 " --> pdb=" O ILE A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 410 through 412 Processing sheet with id= G, first strand: chain 'A' and resid 536 through 538 Processing sheet with id= H, first strand: chain 'B' and resid 60 through 65 removed outlier: 6.411A pdb=" N GLY B 89 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE B 33 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 91 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY B 35 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY B 93 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 163 through 165 removed outlier: 3.786A pdb=" N ILE B 165 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 246 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 221 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 248 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 332 through 335 removed outlier: 4.268A pdb=" N VAL B 333 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 394 through 397 Processing sheet with id= L, first strand: chain 'B' and resid 406 through 409 Processing sheet with id= M, first strand: chain 'B' and resid 475 through 477 removed outlier: 3.740A pdb=" N ILE B 477 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 521 through 524 Processing sheet with id= O, first strand: chain 'B' and resid 353 through 358 removed outlier: 3.606A pdb=" N LEU B 353 " --> pdb=" O TRP B 370 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 357 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS B 366 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 60 through 66 removed outlier: 6.113A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL C 92 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE C 119 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.287A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 267 through 271 removed outlier: 4.112A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 397 through 402 removed outlier: 6.737A pdb=" N THR C 471 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE C 400 " --> pdb=" O THR C 471 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU C 473 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR C 402 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS C 475 " --> pdb=" O THR C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 410 through 413 Processing sheet with id= U, first strand: chain 'C' and resid 525 through 527 Processing sheet with id= V, first strand: chain 'C' and resid 727 through 730 removed outlier: 4.451A pdb=" N ILE C 538 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 532 through 536 removed outlier: 3.707A pdb=" N LYS C 532 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 536 " --> pdb=" O PHE C 752 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE C 752 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 60 through 68 removed outlier: 3.533A pdb=" N VAL D 34 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY D 91 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE D 35 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL D 93 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL D 37 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY D 95 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE D 94 " --> pdb=" O PRO D 117 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU D 119 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ASP D 96 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 197 through 200 removed outlier: 7.261A pdb=" N ILE D 166 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N LEU D 200 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR D 168 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR D 250 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU D 225 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 252 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 273 through 277 Processing sheet with id= AA, first strand: chain 'D' and resid 400 through 403 removed outlier: 6.191A pdb=" N ASP D 470 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N THR D 403 " --> pdb=" O ASP D 470 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR D 472 " --> pdb=" O THR D 403 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 411 through 414 removed outlier: 3.856A pdb=" N ARG D 448 " --> pdb=" O CYS D 429 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 481 through 483 Processing sheet with id= AD, first strand: chain 'D' and resid 722 through 725 removed outlier: 3.675A pdb=" N VAL D 531 " --> pdb=" O VAL D 742 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 4 through 7 Processing sheet with id= AF, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.759A pdb=" N UNK F 104 " --> pdb=" O UNK F 11 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N UNK F 13 " --> pdb=" O UNK F 104 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N UNK F 106 " --> pdb=" O UNK F 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 86 through 91 removed outlier: 5.532A pdb=" N UNK F 38 " --> pdb=" O UNK F 47 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N UNK F 47 " --> pdb=" O UNK F 38 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.187A pdb=" N UNK F 175 " --> pdb=" O UNK F 165 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 154 through 156 removed outlier: 4.022A pdb=" N UNK F 149 " --> pdb=" O UNK F 156 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 3 through 7 Processing sheet with id= AK, first strand: chain 'G' and resid 113 through 115 removed outlier: 5.852A pdb=" N UNK G 38 " --> pdb=" O UNK G 47 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N UNK G 47 " --> pdb=" O UNK G 38 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N UNK G 40 " --> pdb=" O UNK G 45 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N UNK G 45 " --> pdb=" O UNK G 40 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 126 through 131 removed outlier: 5.418A pdb=" N UNK G 177 " --> pdb=" O UNK G 146 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N UNK G 180 " --> pdb=" O UNK G 168 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 152 through 156 Processing sheet with id= AN, first strand: chain 'G' and resid 171 through 173 1039 hydrogen bonds defined for protein. 2694 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: 10.17 Time building geometry restraints manager: 11.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5513 1.33 - 1.45: 6659 1.45 - 1.58: 12465 1.58 - 1.71: 1 1.71 - 1.84: 182 Bond restraints: 24820 Sorted by residual: bond pdb=" CA PRO A 263 " pdb=" C PRO A 263 " ideal model delta sigma weight residual 1.520 1.684 -0.164 1.42e-02 4.96e+03 1.34e+02 bond pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta sigma weight residual 1.469 1.550 -0.081 1.28e-02 6.10e+03 4.00e+01 bond pdb=" CA ALA B 141 " pdb=" C ALA B 141 " ideal model delta sigma weight residual 1.520 1.450 0.070 1.22e-02 6.72e+03 3.32e+01 bond pdb=" N PHE B 178 " pdb=" CA PHE B 178 " ideal model delta sigma weight residual 1.459 1.394 0.065 1.19e-02 7.06e+03 3.01e+01 bond pdb=" N UNK F 78 " pdb=" CA UNK F 78 " ideal model delta sigma weight residual 1.458 1.361 0.097 1.90e-02 2.77e+03 2.63e+01 ... (remaining 24815 not shown) Histogram of bond angle deviations from ideal: 88.32 - 97.70: 11 97.70 - 107.09: 1166 107.09 - 116.48: 16560 116.48 - 125.86: 15956 125.86 - 135.25: 438 Bond angle restraints: 34131 Sorted by residual: angle pdb=" N THR B 200 " pdb=" CA THR B 200 " pdb=" C THR B 200 " ideal model delta sigma weight residual 111.28 126.70 -15.42 1.09e+00 8.42e-01 2.00e+02 angle pdb=" N VAL D 613 " pdb=" CA VAL D 613 " pdb=" C VAL D 613 " ideal model delta sigma weight residual 110.42 122.44 -12.02 9.60e-01 1.09e+00 1.57e+02 angle pdb=" C SER A 754 " pdb=" N GLY A 755 " pdb=" CA GLY A 755 " ideal model delta sigma weight residual 121.45 133.95 -12.50 1.06e+00 8.90e-01 1.39e+02 angle pdb=" N SER D 534 " pdb=" CA SER D 534 " pdb=" C SER D 534 " ideal model delta sigma weight residual 111.14 123.15 -12.01 1.08e+00 8.57e-01 1.24e+02 angle pdb=" N GLN B 67 " pdb=" CA GLN B 67 " pdb=" C GLN B 67 " ideal model delta sigma weight residual 111.36 122.92 -11.56 1.09e+00 8.42e-01 1.13e+02 ... (remaining 34126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 13574 17.83 - 35.66: 751 35.66 - 53.49: 326 53.49 - 71.32: 84 71.32 - 89.15: 19 Dihedral angle restraints: 14754 sinusoidal: 4233 harmonic: 10521 Sorted by residual: dihedral pdb=" CA UNK G 148 " pdb=" C UNK G 148 " pdb=" N UNK G 149 " pdb=" CA UNK G 149 " ideal model delta harmonic sigma weight residual 180.00 107.65 72.35 0 5.00e+00 4.00e-02 2.09e+02 dihedral pdb=" C UNK F 67 " pdb=" N UNK F 67 " pdb=" CA UNK F 67 " pdb=" CB UNK F 67 " ideal model delta harmonic sigma weight residual -122.60 -157.68 35.08 0 2.50e+00 1.60e-01 1.97e+02 dihedral pdb=" N UNK F 67 " pdb=" C UNK F 67 " pdb=" CA UNK F 67 " pdb=" CB UNK F 67 " ideal model delta harmonic sigma weight residual 122.80 157.40 -34.60 0 2.50e+00 1.60e-01 1.92e+02 ... (remaining 14751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.312: 4177 0.312 - 0.625: 72 0.625 - 0.937: 2 0.937 - 1.249: 0 1.249 - 1.561: 1 Chirality restraints: 4252 Sorted by residual: chirality pdb=" CA UNK F 67 " pdb=" N UNK F 67 " pdb=" C UNK F 67 " pdb=" CB UNK F 67 " both_signs ideal model delta sigma weight residual False 2.52 0.96 1.56 2.00e-01 2.50e+01 6.09e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.73e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.68e+01 ... (remaining 4249 not shown) Planarity restraints: 4426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG N 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.508 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.335 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG H 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.499 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.315 2.00e-02 2.50e+03 2.71e-01 9.18e+02 pdb=" C7 NAG K 1 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.011 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.467 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.211 2.00e-02 2.50e+03 ... (remaining 4423 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.84: 18 1.84 - 2.60: 697 2.60 - 3.37: 35174 3.37 - 4.13: 55779 4.13 - 4.90: 96321 Nonbonded interactions: 187989 Sorted by model distance: nonbonded pdb=" OH TYR A 679 " pdb=" CD1 ILE A 728 " model vdw 1.072 3.460 nonbonded pdb=" CZ TYR A 679 " pdb=" CD1 ILE A 728 " model vdw 1.142 3.680 nonbonded pdb=" SD MET D 302 " pdb=" CG PRO D 310 " model vdw 1.215 3.800 nonbonded pdb=" O GLY C 825 " pdb=" CG2 ILE C 829 " model vdw 1.425 3.460 nonbonded pdb=" O ASN C 273 " pdb=" CD2 HIS C 280 " model vdw 1.427 3.260 ... (remaining 187984 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 23 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 75 or (resid 76 and ( \ name N or name CA or name C or name O or name CB )) or resid 77 through 79 or (r \ esid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thr \ ough 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or \ resid 95 through 100 or (resid 101 through 103 and (name N or name CA or name C \ or name O or name CB )) or resid 104 through 129 or (resid 130 and (name N or n \ ame CA or name C or name O or name CB )) or resid 131 through 143 or (resid 144 \ and (name N or name CA or name C or name O or name CB )) or resid 145 or (resid \ 146 through 149 and (name N or name CA or name C or name O or name CB )) or resi \ d 150 or (resid 151 through 155 and (name N or name CA or name C or name O or na \ me CB )) or resid 156 or (resid 157 through 162 and (name N or name CA or name C \ or name O or name CB )) or resid 163 through 168 or (resid 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 176 or (resid 177 \ through 178 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 9 through 180 or (resid 181 through 182 and (name N or name CA or name C or name \ O or name CB )) or resid 183 or (resid 184 through 193 and (name N or name CA o \ r name C or name O or name CB )) or resid 194 through 197 or (resid 198 and (nam \ e N or name CA or name C or name O or name CB )) or resid 199 through 200 or (re \ sid 201 through 202 and (name N or name CA or name C or name O or name CB )) or \ resid 203 through 209 or (resid 210 through 211 and (name N or name CA or name C \ or name O or name CB )) or resid 212 or (resid 213 through 220 and (name N or n \ ame CA or name C or name O or name CB )) or resid 221 through 223 or (resid 224 \ through 225 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 6 through 231 or (resid 232 through 233 and (name N or name CA or name C or name \ O or name CB )) or resid 234 through 239 or (resid 240 and (name N or name CA o \ r name C or name O or name CB )) or resid 241 through 244 or (resid 245 through \ 249 and (name N or name CA or name C or name O or name CB )) or resid 250 or (re \ sid 251 through 255 and (name N or name CA or name C or name O or name CB )) or \ resid 256 through 258 or (resid 259 and (name N or name CA or name C or name O o \ r name CB )) or resid 260 through 265 or (resid 266 through 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 or (resid 269 through 272 \ and (name N or name CA or name C or name O or name CB )) or resid 273 through 34 \ 5 or (resid 346 through 347 and (name N or name CA or name C or name O or name C \ B )) or resid 348 through 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB )) or resid 352 through 355 or (resid 356 through 363 and (nam \ e N or name CA or name C or name O or name CB )) or resid 364 through 372 or (re \ sid 373 through 381 and (name N or name CA or name C or name O or name CB )) or \ resid 382 through 415 or (resid 416 and (name N or name CA or name C or name O o \ r name CB )) or resid 417 through 447 or (resid 448 and (name N or name CA or na \ me C or name O or name CB )) or resid 449 through 466 or (resid 467 and (name N \ or name CA or name C or name O or name CB )) or resid 468 through 495 or (resid \ 496 through 497 and (name N or name CA or name C or name O or name CB )) or resi \ d 498 through 547 or (resid 548 through 554 and (name N or name CA or name C or \ name O or name CB )) or resid 555 or (resid 556 through 557 and (name N or name \ CA or name C or name O or name CB )) or resid 558 through 560 or (resid 561 and \ (name N or name CA or name C or name O or name CB )) or resid 562 through 577 or \ (resid 578 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 9 or (resid 580 through 581 and (name N or name CA or name C or name O or name C \ B )) or resid 582 through 601 or (resid 602 and (name N or name CA or name C or \ name O or name CB )) or resid 603 through 606 or (resid 607 and (name N or name \ CA or name C or name O or name CB )) or resid 608 through 610 or (resid 611 thro \ ugh 615 and (name N or name CA or name C or name O or name CB )) or resid 616 th \ rough 624 or (resid 625 through 628 and (name N or name CA or name C or name O o \ r name CB )) or resid 629 through 653 or (resid 654 through 657 and (name N or n \ ame CA or name C or name O or name CB )) or resid 658 through 662 or (resid 663 \ and (name N or name CA or name C or name O or name CB )) or resid 664 through 67 \ 4 or (resid 675 through 676 and (name N or name CA or name C or name O or name C \ B )) or resid 677 through 692 or (resid 693 and (name N or name CA or name C or \ name O or name CB )) or resid 694 through 699 or (resid 700 and (name N or name \ CA or name C or name O or name CB )) or resid 701 or (resid 702 and (name N or n \ ame CA or name C or name O or name CB )) or resid 703 through 704 or (resid 705 \ through 706 and (name N or name CA or name C or name O or name CB )) or resid 70 \ 7 through 738 or (resid 739 through 741 and (name N or name CA or name C or name \ O or name CB )) or resid 742 through 792 or (resid 793 and (name N or name CA o \ r name C or name O or name CB )) or resid 794 through 805 or (resid 806 through \ 810 and (name N or name CA or name C or name O or name CB )) or resid 811 throug \ h 832 or (resid 833 through 836 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'C' and (resid 23 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 113 or (resid 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 through 271 or (resid 272 \ and (name N or name CA or name C or name O or name CB )) or resid 273 through 32 \ 2 or (resid 323 and (name N or name CA or name C or name O or name CB )) or resi \ d 324 through 389 or (resid 390 and (name N or name CA or name C or name O or na \ me CB )) or resid 391 through 394 or (resid 395 through 396 and (name N or name \ CA or name C or name O or name CB )) or resid 397 through 402 or (resid 403 and \ (name N or name CA or name C or name O or name CB )) or resid 404 or (resid 405 \ and (name N or name CA or name C or name O or name CB )) or resid 406 through 41 \ 1 or (resid 412 and (name N or name CA or name C or name O or name CB )) or resi \ d 413 or (resid 414 through 416 and (name N or name CA or name C or name O or na \ me CB )) or resid 417 through 420 or (resid 421 through 424 and (name N or name \ CA or name C or name O or name CB )) or resid 425 through 426 or (resid 427 and \ (name N or name CA or name C or name O or name CB )) or resid 428 or (resid 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 or (resid \ 431 and (name N or name CA or name C or name O or name CB )) or resid 432 or (re \ sid 433 and (name N or name CA or name C or name O or name CB )) or resid 434 th \ rough 471 or (resid 472 through 473 and (name N or name CA or name C or name O o \ r name CB )) or resid 474 through 475 or (resid 476 and (name N or name CA or na \ me C or name O or name CB )) or resid 477 through 478 or (resid 479 and (name N \ or name CA or name C or name O or name CB )) or resid 480 or (resid 481 and (nam \ e N or name CA or name C or name O or name CB )) or resid 482 through 483 or (re \ sid 484 through 497 and (name N or name CA or name C or name O or name CB )) or \ resid 498 or (resid 499 and (name N or name CA or name C or name O or name CB )) \ or resid 500 through 506 or (resid 507 through 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 through 518 or (resid 519 through 520 \ and (name N or name CA or name C or name O or name CB )) or resid 521 through 52 \ 5 or (resid 526 and (name N or name CA or name C or name O or name CB )) or resi \ d 527 through 528 or (resid 529 and (name N or name CA or name C or name O or na \ me CB )) or resid 530 through 582 or resid 600 through 623 or (resid 624 through \ 628 and (name N or name CA or name C or name O or name CB )) or resid 629 throu \ gh 631 or (resid 632 and (name N or name CA or name C or name O or name CB )) or \ resid 633 through 713 or (resid 714 through 716 and (name N or name CA or name \ C or name O or name CB )) or resid 717 through 719 or (resid 720 through 723 and \ (name N or name CA or name C or name O or name CB )) or resid 724 or (resid 725 \ through 727 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 28 through 733 or (resid 734 and (name N or name CA or name C or name O or name \ CB )) or resid 735 through 736 or (resid 737 through 741 and (name N or name CA \ or name C or name O or name CB )) or resid 742 or (resid 743 and (name N or name \ CA or name C or name O or name CB )) or resid 744 through 749 or (resid 750 thr \ ough 751 and (name N or name CA or name C or name O or name CB )) or resid 752 t \ hrough 782 or (resid 783 through 784 and (name N or name CA or name C or name O \ or name CB )) or resid 785 through 804 or (resid 805 through 810 and (name N or \ name CA or name C or name O or name CB )) or resid 811 through 836)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 2 through 215) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.010 Extract box with map and model: 5.080 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 67.520 Find NCS groups from input model: 1.460 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 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 0.164 24820 Z= 0.727 Angle : 1.837 36.685 34131 Z= 1.207 Chirality : 0.104 1.561 4252 Planarity : 0.018 0.290 4418 Dihedral : 14.829 84.607 7872 Min Nonbonded Distance : 1.072 Molprobity Statistics. All-atom Clashscore : 54.88 Ramachandran Plot: Outliers : 1.01 % Allowed : 4.48 % Favored : 94.51 % Rotamer: Outliers : 10.98 % Allowed : 8.69 % Favored : 80.33 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 1.57 % 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: -0.55 (0.14), residues: 3169 helix: 0.51 (0.14), residues: 1178 sheet: -0.26 (0.29), residues: 319 loop : -1.02 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 766 HIS 0.010 0.001 HIS A 101 PHE 0.036 0.002 PHE C 408 TYR 0.058 0.004 TYR C 472 ARG 0.018 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 113 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.5454 (mm) REVERT: A 469 ASP cc_start: 0.9253 (OUTLIER) cc_final: 0.8976 (p0) REVERT: C 477 VAL cc_start: 0.6223 (OUTLIER) cc_final: 0.5565 (p) REVERT: C 695 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7901 (p) REVERT: D 72 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7420 (t0) REVERT: D 152 MET cc_start: 0.8053 (mtp) cc_final: 0.6806 (mmm) REVERT: D 543 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.6280 (p90) REVERT: D 558 MET cc_start: 0.8425 (tpt) cc_final: 0.8097 (ttt) REVERT: D 794 CYS cc_start: 0.6619 (OUTLIER) cc_final: 0.6325 (p) outliers start: 206 outliers final: 49 residues processed: 304 average time/residue: 0.3505 time to fit residues: 167.9306 Evaluate side-chains 166 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 110 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 280 optimal weight: 7.9990 chunk 108 optimal weight: 40.0000 chunk 170 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 325 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 196 GLN ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN A 810 ASN ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 350 ASN B 389 HIS B 503 ASN B 662 HIS B 675 GLN ** B 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 86 GLN C 393 GLN C 404 HIS C 451 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 GLN C 725 HIS D 55 HIS D 154 ASN D 306 HIS D 354 HIS D 691 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24820 Z= 0.354 Angle : 0.841 18.375 34131 Z= 0.441 Chirality : 0.049 0.957 4252 Planarity : 0.008 0.173 4418 Dihedral : 7.269 59.873 4104 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.29 % Favored : 95.42 % Rotamer: Outliers : 0.27 % Allowed : 4.32 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % 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: -0.75 (0.14), residues: 3169 helix: 0.28 (0.13), residues: 1255 sheet: -0.72 (0.24), residues: 400 loop : -1.05 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 597 HIS 0.015 0.002 HIS D 55 PHE 0.042 0.003 PHE B 178 TYR 0.033 0.003 TYR D 333 ARG 0.007 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8490 (tmm) cc_final: 0.8101 (tmm) REVERT: A 700 MET cc_start: 0.8494 (mpp) cc_final: 0.8203 (mmm) REVERT: B 548 MET cc_start: 0.8347 (tpt) cc_final: 0.7885 (tpp) REVERT: C 354 MET cc_start: 0.9018 (mmp) cc_final: 0.8659 (mmm) REVERT: D 152 MET cc_start: 0.7053 (mtp) cc_final: 0.6679 (mmm) REVERT: D 555 MET cc_start: 0.5062 (tpt) cc_final: 0.4451 (tpt) outliers start: 5 outliers final: 1 residues processed: 116 average time/residue: 0.3085 time to fit residues: 61.6708 Evaluate side-chains 112 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 40.0000 chunk 100 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 325 optimal weight: 30.0000 chunk 351 optimal weight: 50.0000 chunk 290 optimal weight: 5.9990 chunk 322 optimal weight: 30.0000 chunk 111 optimal weight: 0.0970 chunk 261 optimal weight: 5.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 HIS B 754 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 HIS C 707 HIS D 690 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 24820 Z= 0.261 Angle : 0.691 14.010 34131 Z= 0.357 Chirality : 0.044 0.638 4252 Planarity : 0.006 0.153 4418 Dihedral : 6.539 59.222 4104 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.74 % Favored : 94.04 % Rotamer: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % 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: -0.45 (0.14), residues: 3169 helix: 0.59 (0.14), residues: 1271 sheet: -0.48 (0.25), residues: 364 loop : -0.96 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 496 HIS 0.010 0.001 HIS A 146 PHE 0.025 0.002 PHE B 178 TYR 0.020 0.002 TYR A 679 ARG 0.005 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.8988 (ptp) cc_final: 0.8779 (ptt) REVERT: D 152 MET cc_start: 0.6987 (mtp) cc_final: 0.6657 (mmm) REVERT: D 558 MET cc_start: 0.7841 (ttp) cc_final: 0.7553 (ttt) outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 0.3096 time to fit residues: 60.6525 Evaluate side-chains 111 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 20.0000 chunk 244 optimal weight: 30.0000 chunk 169 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 326 optimal weight: 50.0000 chunk 346 optimal weight: 50.0000 chunk 170 optimal weight: 5.9990 chunk 309 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN B 684 ASN C 196 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 199 HIS D 306 HIS D 810 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 24820 Z= 0.294 Angle : 0.690 13.952 34131 Z= 0.359 Chirality : 0.044 0.540 4252 Planarity : 0.006 0.143 4418 Dihedral : 6.443 59.048 4104 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.96 % Favored : 93.82 % Rotamer: Outliers : 0.27 % Allowed : 2.72 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % 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: -0.52 (0.14), residues: 3169 helix: 0.53 (0.14), residues: 1278 sheet: -0.66 (0.25), residues: 389 loop : -0.98 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 766 HIS 0.007 0.002 HIS B 473 PHE 0.036 0.002 PHE C 815 TYR 0.027 0.002 TYR A 679 ARG 0.005 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 555 MET cc_start: 0.5950 (tpt) cc_final: 0.4696 (tpt) outliers start: 5 outliers final: 2 residues processed: 114 average time/residue: 0.2947 time to fit residues: 58.8137 Evaluate side-chains 111 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 295 optimal weight: 1.9990 chunk 239 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 176 optimal weight: 6.9990 chunk 310 optimal weight: 0.0170 chunk 87 optimal weight: 10.0000 overall best weight: 5.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 210 GLN C 523 GLN D 122 HIS D 199 HIS ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 24820 Z= 0.237 Angle : 0.633 10.503 34131 Z= 0.326 Chirality : 0.043 0.491 4252 Planarity : 0.005 0.135 4418 Dihedral : 6.159 59.563 4104 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.66 % Favored : 93.15 % Rotamer: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % 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: -0.41 (0.15), residues: 3169 helix: 0.63 (0.14), residues: 1290 sheet: -0.73 (0.25), residues: 389 loop : -0.90 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 766 HIS 0.007 0.001 HIS A 146 PHE 0.019 0.002 PHE D 631 TYR 0.022 0.001 TYR B 157 ARG 0.003 0.001 ARG B 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 2.721 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: D 555 MET cc_start: 0.6670 (tpt) cc_final: 0.6444 (tpt) REVERT: D 558 MET cc_start: 0.7813 (ptm) cc_final: 0.7600 (ptm) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.3084 time to fit residues: 59.6240 Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 8.9990 chunk 311 optimal weight: 8.9990 chunk 68 optimal weight: 0.0670 chunk 203 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 346 optimal weight: 50.0000 chunk 287 optimal weight: 50.0000 chunk 160 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 684 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 24820 Z= 0.206 Angle : 0.603 9.477 34131 Z= 0.309 Chirality : 0.043 0.749 4252 Planarity : 0.005 0.128 4418 Dihedral : 6.062 59.695 4104 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.96 % Favored : 93.82 % Rotamer: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % 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: -0.33 (0.15), residues: 3169 helix: 0.73 (0.14), residues: 1299 sheet: -0.67 (0.26), residues: 391 loop : -0.90 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 766 HIS 0.007 0.001 HIS A 146 PHE 0.025 0.002 PHE C 637 TYR 0.020 0.001 TYR B 157 ARG 0.014 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 548 MET cc_start: 0.8752 (tmm) cc_final: 0.8365 (mtt) REVERT: D 555 MET cc_start: 0.6886 (tpt) cc_final: 0.6509 (tpt) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2911 time to fit residues: 56.1709 Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 50.0000 chunk 39 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 291 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 345 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 210 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 24820 Z= 0.182 Angle : 0.576 9.470 34131 Z= 0.292 Chirality : 0.042 0.638 4252 Planarity : 0.004 0.122 4418 Dihedral : 5.834 59.021 4104 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.12 % Favored : 93.66 % Rotamer: Outliers : 0.05 % Allowed : 0.96 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % 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 (0.15), residues: 3169 helix: 0.92 (0.14), residues: 1299 sheet: -0.64 (0.26), residues: 405 loop : -0.86 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.005 0.001 HIS A 146 PHE 0.017 0.001 PHE C 296 TYR 0.013 0.001 TYR A 392 ARG 0.002 0.000 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 548 MET cc_start: 0.8704 (tmm) cc_final: 0.8438 (mtt) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2910 time to fit residues: 55.6746 Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 67 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 219 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 170 optimal weight: 0.1980 chunk 32 optimal weight: 0.0470 chunk 271 optimal weight: 40.0000 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 ASN D 690 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 24820 Z= 0.150 Angle : 0.561 9.489 34131 Z= 0.284 Chirality : 0.042 0.578 4252 Planarity : 0.004 0.118 4418 Dihedral : 5.627 59.201 4104 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.70 % Favored : 95.08 % Rotamer: Outliers : 0.05 % Allowed : 0.91 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % 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: -0.04 (0.15), residues: 3169 helix: 1.10 (0.14), residues: 1296 sheet: -0.55 (0.26), residues: 405 loop : -0.85 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 628 HIS 0.006 0.001 HIS B 160 PHE 0.028 0.001 PHE D 630 TYR 0.014 0.001 TYR C 576 ARG 0.005 0.000 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 MET cc_start: 0.7780 (ptt) cc_final: 0.7257 (ppp) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2993 time to fit residues: 57.7325 Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 20.0000 chunk 330 optimal weight: 50.0000 chunk 301 optimal weight: 8.9990 chunk 321 optimal weight: 20.0000 chunk 193 optimal weight: 50.0000 chunk 140 optimal weight: 30.0000 chunk 252 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 304 optimal weight: 30.0000 chunk 320 optimal weight: 20.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 196 GLN A 311 ASN A 794 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN D 214 GLN ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 775 GLN D 795 HIS D 833 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.7337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 24820 Z= 0.425 Angle : 0.831 13.883 34131 Z= 0.439 Chirality : 0.046 0.588 4252 Planarity : 0.006 0.116 4418 Dihedral : 6.391 59.574 4104 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 33.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.70 % Favored : 92.08 % Rotamer: Outliers : 0.11 % Allowed : 0.64 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3169 helix: 0.12 (0.13), residues: 1296 sheet: -1.10 (0.26), residues: 399 loop : -1.19 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 190 HIS 0.016 0.002 HIS A 703 PHE 0.043 0.003 PHE A 531 TYR 0.029 0.003 TYR A 679 ARG 0.008 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.8371 (mmp) cc_final: 0.8140 (mmm) REVERT: A 605 MET cc_start: 0.9261 (ptp) cc_final: 0.9031 (ptt) REVERT: A 639 MET cc_start: 0.8128 (ptt) cc_final: 0.7812 (ptt) REVERT: D 558 MET cc_start: 0.8708 (ptp) cc_final: 0.8372 (ptp) outliers start: 2 outliers final: 1 residues processed: 110 average time/residue: 0.2943 time to fit residues: 57.1625 Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 356 optimal weight: 50.0000 chunk 328 optimal weight: 50.0000 chunk 284 optimal weight: 40.0000 chunk 29 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 794 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 760 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24820 Z= 0.255 Angle : 0.640 11.928 34131 Z= 0.334 Chirality : 0.042 0.607 4252 Planarity : 0.005 0.113 4418 Dihedral : 6.175 59.761 4104 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.78 % Favored : 92.99 % Rotamer: Outliers : 0.05 % Allowed : 0.27 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % 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: -0.78 (0.15), residues: 3169 helix: 0.46 (0.14), residues: 1291 sheet: -1.06 (0.26), residues: 381 loop : -1.21 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 628 HIS 0.009 0.001 HIS A 146 PHE 0.031 0.002 PHE D 631 TYR 0.016 0.002 TYR A 793 ARG 0.004 0.001 ARG B 669 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.8385 (mmp) cc_final: 0.8148 (mmm) REVERT: A 639 MET cc_start: 0.8122 (ptt) cc_final: 0.7874 (ptt) REVERT: C 354 MET cc_start: 0.9630 (mmm) cc_final: 0.9399 (mmm) REVERT: D 624 MET cc_start: 0.7817 (ptt) cc_final: 0.7600 (ptp) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2820 time to fit residues: 54.1432 Evaluate side-chains 109 residues out of total 2773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 0.8980 chunk 302 optimal weight: 0.1980 chunk 87 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 284 optimal weight: 30.0000 chunk 119 optimal weight: 20.0000 chunk 292 optimal weight: 0.0770 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.027706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.020412 restraints weight = 494930.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 102)---------------| | r_work = 0.2849 r_free = 0.2849 target = 0.020465 restraints weight = 407393.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.020748 restraints weight = 328564.346| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24820 Z= 0.173 Angle : 0.582 10.786 34131 Z= 0.298 Chirality : 0.042 0.576 4252 Planarity : 0.004 0.110 4418 Dihedral : 5.886 59.526 4104 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.01 % Favored : 92.77 % Rotamer: Outliers : 0.05 % Allowed : 0.11 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % 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: -0.45 (0.15), residues: 3169 helix: 0.83 (0.14), residues: 1312 sheet: -0.88 (0.26), residues: 410 loop : -1.13 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 628 HIS 0.006 0.001 HIS C 778 PHE 0.030 0.001 PHE D 631 TYR 0.013 0.001 TYR A 679 ARG 0.003 0.000 ARG C 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3838.21 seconds wall clock time: 70 minutes 48.28 seconds (4248.28 seconds total)