Starting phenix.real_space_refine (version: dev) on Wed Mar 15 01:06:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2023/7m3g_23654_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2023/7m3g_23654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2023/7m3g_23654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2023/7m3g_23654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2023/7m3g_23654_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2023/7m3g_23654_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B GLU 507": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B ASP 674": "OD1" <-> "OD2" Residue "B TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 767": "OE1" <-> "OE2" Residue "B PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 870": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 13298 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6485 Classifications: {'peptide': 821} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 31, 'TRANS': 789} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6375 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 31, 'TRANS': 772} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Modifications used: {'PEPT-D': 7} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Modifications used: {'PEPT-D': 7} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} 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 chiralities: 2 Chain: "F" 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 chiralities: 2 Chain: "G" 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 93 Unusual residues: {' CA': 3, 'H43': 1, 'NAG': 3, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 905 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Unusual residues: {' CA': 1, 'H43': 1, 'NAG': 2, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B 904 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.65, per 1000 atoms: 0.58 Number of scatterers: 13298 At special positions: 0 Unit cell: (99.9, 92.13, 192.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 75 16.00 P 2 15.00 O 2449 8.00 N 2152 7.00 C 8616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.04 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG DCY C 2 " distance=2.04 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.04 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG DCY D 2 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.04 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 902 " - " ASN A 468 " " NAG A 903 " - " ASN A 488 " " NAG A 904 " - " ASN A 594 " " NAG B 902 " - " ASN B 468 " " NAG B 903 " - " ASN B 594 " " NAG E 1 " - " ASN A 261 " " NAG F 1 " - " ASN A 541 " " NAG G 1 " - " ASN B 261 " " NAG H 1 " - " ASN B 488 " " NAG I 1 " - " ASN B 541 " Time building additional restraints: 6.21 Conformation dependent library (CDL) restraints added in 1.9 seconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DCY C 2 " pdb=" CB DAL C 3 " pdb=" CB DAR C 4 " pdb=" CB DAR C 5 " pdb=" CB DAR C 6 " pdb=" CB DAL C 7 " pdb=" CB DAR C 8 " pdb=" CB DCY D 2 " pdb=" CB DAL D 3 " pdb=" CB DAR D 4 " pdb=" CB DAR D 5 " pdb=" CB DAR D 6 " pdb=" CB DAL D 7 " pdb=" CB DAR D 8 " Number of C-beta restraints generated: 3064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 14 sheets defined 41.7% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.730A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.605A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 removed outlier: 3.658A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.793A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 5.103A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.832A pdb=" N LYS A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 611 through 636 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 650 through 668 removed outlier: 4.163A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 698 removed outlier: 3.893A pdb=" N VAL A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 745 removed outlier: 4.354A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 793 Processing helix chain 'A' and resid 803 through 820 Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.510A pdb=" N SER A 827 " --> pdb=" O PRO A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 removed outlier: 3.506A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 removed outlier: 3.725A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 872 No H-bonds generated for 'chain 'A' and resid 869 through 872' Processing helix chain 'A' and resid 880 through 886 Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.748A pdb=" N MET B 74 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 116 through 123 removed outlier: 3.650A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.781A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 191 through 203 removed outlier: 3.674A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 308 through 314 removed outlier: 5.022A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 346 through 356 removed outlier: 4.070A pdb=" N LYS B 349 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 350 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 356 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 611 through 636 Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.799A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 666 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 698 removed outlier: 4.163A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 745 removed outlier: 4.156A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 792 removed outlier: 3.837A pdb=" N THR B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 820 Processing helix chain 'B' and resid 822 through 824 No H-bonds generated for 'chain 'B' and resid 822 through 824' Processing helix chain 'B' and resid 831 through 853 removed outlier: 3.984A pdb=" N ALA B 835 " --> pdb=" O PHE B 832 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA B 840 " --> pdb=" O GLU B 837 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 845 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 849 " --> pdb=" O PHE B 846 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 851 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 853 " --> pdb=" O ALA B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 860 Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.299A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU A 37 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 143 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLY A 143 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL A 165 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.483A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.442A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= E, first strand: chain 'A' and resid 550 through 554 Processing sheet with id= F, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= G, first strand: chain 'A' and resid 602 through 604 Processing sheet with id= H, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.442A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.477A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.566A pdb=" N GLY B 509 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= L, first strand: chain 'B' and resid 550 through 554 Processing sheet with id= M, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= N, first strand: chain 'B' and resid 602 through 604 485 hydrogen bonds defined for protein. 1362 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: 4.23 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4047 1.34 - 1.46: 3424 1.46 - 1.58: 6061 1.58 - 1.71: 2 1.71 - 1.83: 89 Bond restraints: 13623 Sorted by residual: bond pdb=" C11 H43 A 901 " pdb=" N12 H43 A 901 " ideal model delta sigma weight residual 1.454 1.574 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C13 H43 A 901 " pdb=" N12 H43 A 901 " ideal model delta sigma weight residual 1.459 1.563 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C11 H43 B 901 " pdb=" N12 H43 B 901 " ideal model delta sigma weight residual 1.454 1.553 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C8 H43 A 901 " pdb=" N9 H43 A 901 " ideal model delta sigma weight residual 1.367 1.465 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C8 H43 B 901 " pdb=" N9 H43 B 901 " ideal model delta sigma weight residual 1.367 1.464 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 13618 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.53: 317 106.53 - 113.50: 7215 113.50 - 120.48: 5696 120.48 - 127.46: 5112 127.46 - 134.44: 142 Bond angle restraints: 18482 Sorted by residual: angle pdb=" CA PRO B 641 " pdb=" N PRO B 641 " pdb=" CD PRO B 641 " ideal model delta sigma weight residual 112.00 104.81 7.19 1.40e+00 5.10e-01 2.64e+01 angle pdb=" CB MET B 734 " pdb=" CG MET B 734 " pdb=" SD MET B 734 " ideal model delta sigma weight residual 112.70 126.87 -14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" CA PRO B 748 " pdb=" N PRO B 748 " pdb=" CD PRO B 748 " ideal model delta sigma weight residual 112.00 105.43 6.57 1.40e+00 5.10e-01 2.20e+01 angle pdb=" CB ILE B 603 " pdb=" CG1 ILE B 603 " pdb=" CD1 ILE B 603 " ideal model delta sigma weight residual 113.80 123.60 -9.80 2.10e+00 2.27e-01 2.18e+01 angle pdb=" N GLU B 759 " pdb=" CA GLU B 759 " pdb=" C GLU B 759 " ideal model delta sigma weight residual 114.62 109.48 5.14 1.14e+00 7.69e-01 2.03e+01 ... (remaining 18477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 7629 35.99 - 71.98: 210 71.98 - 107.98: 16 107.98 - 143.97: 0 143.97 - 179.96: 4 Dihedral angle restraints: 7859 sinusoidal: 3112 harmonic: 4747 Sorted by residual: dihedral pdb=" CD DAR D 4 " pdb=" NE DAR D 4 " pdb=" CZ DAR D 4 " pdb=" NH1 DAR D 4 " ideal model delta sinusoidal sigma weight residual 0.00 179.96 -179.96 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD DAR C 8 " pdb=" NE DAR C 8 " pdb=" CZ DAR C 8 " pdb=" NH1 DAR C 8 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD DAR D 5 " pdb=" NE DAR D 5 " pdb=" CZ DAR D 5 " pdb=" NH1 DAR D 5 " ideal model delta sinusoidal sigma weight residual 0.00 -179.70 179.70 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 7856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1678 0.069 - 0.138: 368 0.138 - 0.207: 42 0.207 - 0.276: 3 0.276 - 0.345: 4 Chirality restraints: 2095 Sorted by residual: chirality pdb=" C13 H43 A 901 " pdb=" C14 H43 A 901 " pdb=" C24 H43 A 901 " pdb=" N12 H43 A 901 " both_signs ideal model delta sigma weight residual False -2.34 -2.68 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE A 61 " pdb=" CA ILE A 61 " pdb=" CG1 ILE A 61 " pdb=" CG2 ILE A 61 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C13 H43 B 901 " pdb=" C14 H43 B 901 " pdb=" C24 H43 B 901 " pdb=" N12 H43 B 901 " both_signs ideal model delta sigma weight residual False -2.34 -2.67 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 2092 not shown) Planarity restraints: 2332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 747 " -0.098 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO B 748 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO B 748 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 748 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 640 " -0.096 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO B 641 " 0.244 5.00e-02 4.00e+02 pdb=" CA PRO B 641 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO B 641 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 789 " 0.034 2.00e-02 2.50e+03 2.79e-02 1.36e+01 pdb=" CG PHE A 789 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 789 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 789 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 789 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 789 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 789 " 0.006 2.00e-02 2.50e+03 ... (remaining 2329 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3504 2.80 - 3.33: 11125 3.33 - 3.85: 21263 3.85 - 4.38: 24860 4.38 - 4.90: 42569 Nonbonded interactions: 103321 Sorted by model distance: nonbonded pdb=" O ALA A 548 " pdb=" OG SER A 574 " model vdw 2.281 2.440 nonbonded pdb=" OD1 ASP A 480 " pdb=" N ASP A 484 " model vdw 2.290 2.520 nonbonded pdb=" OD2 ASP B 238 " pdb=" OG SER B 262 " model vdw 2.299 2.440 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.312 2.440 nonbonded pdb=" O GLY A 613 " pdb=" OG1 THR A 617 " model vdw 2.322 2.440 ... (remaining 103316 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 20 through 125 or resid 131 through 566 or (resid 567 and \ (name N or name CA or name C or name O or name CB )) or resid 568 through 704 or \ (resid 705 and (name N or name CA or name C or name O or name CB )) or resid 70 \ 6 through 862 or (resid 863 and (name N or name CA or name C or name O or name C \ B )) or resid 864 through 865 or (resid 866 and (name N or name CA or name C or \ name O or name CB )) or resid 867 through 870 or resid 903 through 906)) selection = (chain 'B' and (resid 20 through 48 or (resid 49 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 362 or resid 391 throug \ h 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) or \ resid 501 through 555 or (resid 556 and (name N or name CA or name C or name O o \ r name CB )) or resid 557 through 725 or (resid 726 and (name N or name CA or na \ me C or name O or name CB )) or resid 727 through 870 or resid 902 through 905)) \ } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 75 5.16 5 C 8616 2.51 5 N 2152 2.21 5 O 2449 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 10.130 Check model and map are aligned: 0.200 Process input model: 37.390 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.007 0.120 13623 Z= 0.446 Angle : 0.960 14.174 18482 Z= 0.527 Chirality : 0.058 0.345 2095 Planarity : 0.008 0.145 2322 Dihedral : 17.072 179.960 4738 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.18), residues: 1609 helix: -0.94 (0.17), residues: 686 sheet: -1.14 (0.32), residues: 223 loop : -1.70 (0.21), residues: 700 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.543 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 170 average time/residue: 1.0005 time to fit residues: 190.6362 Evaluate side-chains 163 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 3 average time/residue: 0.6606 time to fit residues: 4.4461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.0060 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 673 GLN B 253 GLN B 583 ASN B 595 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 13623 Z= 0.230 Angle : 0.581 7.440 18482 Z= 0.309 Chirality : 0.045 0.169 2095 Planarity : 0.005 0.086 2322 Dihedral : 10.741 178.814 1805 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % 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: -1.04 (0.20), residues: 1609 helix: 0.31 (0.19), residues: 699 sheet: -1.10 (0.32), residues: 231 loop : -1.54 (0.22), residues: 679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 24 residues processed: 187 average time/residue: 0.9244 time to fit residues: 195.5719 Evaluate side-chains 177 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 15 residues processed: 10 average time/residue: 0.4671 time to fit residues: 7.8547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN A 753 ASN B 463 HIS B 583 ASN B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 13623 Z= 0.276 Angle : 0.593 7.562 18482 Z= 0.314 Chirality : 0.046 0.182 2095 Planarity : 0.005 0.073 2322 Dihedral : 10.636 179.035 1805 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.20), residues: 1609 helix: 0.73 (0.20), residues: 697 sheet: -1.04 (0.33), residues: 227 loop : -1.45 (0.22), residues: 685 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 161 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 28 residues processed: 193 average time/residue: 0.8928 time to fit residues: 196.1026 Evaluate side-chains 183 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 20 residues processed: 9 average time/residue: 0.3115 time to fit residues: 6.0393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 98 optimal weight: 0.3980 chunk 147 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 13623 Z= 0.296 Angle : 0.599 9.069 18482 Z= 0.316 Chirality : 0.046 0.188 2095 Planarity : 0.005 0.067 2322 Dihedral : 10.545 179.372 1805 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 4.15 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.20), residues: 1609 helix: 0.93 (0.20), residues: 692 sheet: -1.05 (0.32), residues: 227 loop : -1.43 (0.22), residues: 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 158 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 34 residues processed: 199 average time/residue: 0.8447 time to fit residues: 191.9771 Evaluate side-chains 192 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 25 residues processed: 9 average time/residue: 0.3928 time to fit residues: 6.6042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 116 optimal weight: 0.0030 chunk 64 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 13623 Z= 0.247 Angle : 0.570 8.821 18482 Z= 0.300 Chirality : 0.045 0.176 2095 Planarity : 0.004 0.064 2322 Dihedral : 10.436 179.697 1805 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.20), residues: 1609 helix: 1.03 (0.20), residues: 699 sheet: -1.01 (0.33), residues: 227 loop : -1.37 (0.22), residues: 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 166 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 34 residues processed: 203 average time/residue: 0.8819 time to fit residues: 204.9314 Evaluate side-chains 195 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 27 residues processed: 7 average time/residue: 0.2022 time to fit residues: 4.2980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 5.9990 chunk 141 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 0.0060 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13623 Z= 0.194 Angle : 0.543 8.336 18482 Z= 0.283 Chirality : 0.043 0.183 2095 Planarity : 0.004 0.060 2322 Dihedral : 10.326 179.657 1805 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1609 helix: 1.12 (0.20), residues: 703 sheet: -0.94 (0.33), residues: 227 loop : -1.34 (0.22), residues: 679 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 164 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 36 residues processed: 203 average time/residue: 0.8138 time to fit residues: 189.7677 Evaluate side-chains 197 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 8 average time/residue: 0.6359 time to fit residues: 8.1941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13623 Z= 0.218 Angle : 0.556 8.703 18482 Z= 0.290 Chirality : 0.044 0.186 2095 Planarity : 0.004 0.061 2322 Dihedral : 10.275 179.762 1805 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.21), residues: 1609 helix: 1.20 (0.20), residues: 700 sheet: -0.94 (0.33), residues: 227 loop : -1.34 (0.22), residues: 682 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 163 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 37 residues processed: 202 average time/residue: 0.8296 time to fit residues: 192.2847 Evaluate side-chains 199 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 29 residues processed: 9 average time/residue: 0.3435 time to fit residues: 6.0618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 13623 Z= 0.304 Angle : 0.612 9.263 18482 Z= 0.318 Chirality : 0.046 0.191 2095 Planarity : 0.005 0.067 2322 Dihedral : 10.326 179.901 1805 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.21), residues: 1609 helix: 1.20 (0.20), residues: 698 sheet: -0.95 (0.33), residues: 226 loop : -1.34 (0.22), residues: 685 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 37 residues processed: 195 average time/residue: 0.7232 time to fit residues: 161.0504 Evaluate side-chains 198 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 27 residues processed: 11 average time/residue: 0.2322 time to fit residues: 5.1556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 0.0870 chunk 44 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 0.0770 chunk 144 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13623 Z= 0.161 Angle : 0.535 9.028 18482 Z= 0.277 Chirality : 0.043 0.210 2095 Planarity : 0.004 0.057 2322 Dihedral : 10.197 179.883 1805 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.21), residues: 1609 helix: 1.33 (0.20), residues: 699 sheet: -0.89 (0.33), residues: 227 loop : -1.28 (0.23), residues: 683 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 26 residues processed: 196 average time/residue: 0.8227 time to fit residues: 185.5461 Evaluate side-chains 189 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 0.1780 time to fit residues: 2.4860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1414 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: