Starting phenix.real_space_refine on Sat Mar 16 01:06:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2024/7m3g_23654_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2024/7m3g_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_2024/7m3g_23654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2024/7m3g_23654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2024/7m3g_23654_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3g_23654/03_2024/7m3g_23654_updated.pdb" } resolution = 2.5 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= 0.007 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 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. 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-5265/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 dihedrals: 6 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 dihedrals: 6 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 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: "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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.16, per 1000 atoms: 0.54 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: 5.19 Conformation dependent library (CDL) restraints added in 2.2 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: 2.90 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: 5.54 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: 7931 35.99 - 71.98: 244 71.98 - 107.98: 18 107.98 - 143.97: 1 143.97 - 179.96: 4 Dihedral angle restraints: 8198 sinusoidal: 3451 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 8195 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 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.820 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.400 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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= 0.447 Angle : 0.961 14.174 18482 Z= 0.527 Chirality : 0.058 0.345 2095 Planarity : 0.008 0.145 2322 Dihedral : 17.275 179.960 5077 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 % Allowed : 18.54 % Favored : 80.53 % Cbeta Deviations : 0.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 675 HIS 0.006 0.002 HIS B 338 PHE 0.063 0.003 PHE A 789 TYR 0.021 0.003 TYR A 421 ARG 0.011 0.001 ARG A 648 *********************** 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 : 1.532 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 170 average time/residue: 0.9606 time to fit residues: 183.3683 Evaluate side-chains 163 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 697 VAL 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: 0.9980 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: 0.6980 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 673 GLN B 253 GLN B 583 ASN B 595 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0713 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= 0.230 Angle : 0.593 7.616 18482 Z= 0.314 Chirality : 0.045 0.182 2095 Planarity : 0.005 0.088 2322 Dihedral : 11.597 178.862 2159 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.01 % Allowed : 17.25 % Favored : 79.74 % Cbeta Deviations : 0.00 % 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: -1.08 (0.20), residues: 1609 helix: 0.27 (0.19), residues: 698 sheet: -1.06 (0.33), residues: 223 loop : -1.58 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.044 0.002 PHE A 789 TYR 0.020 0.002 TYR A 421 ARG 0.005 0.000 ARG A 648 *********************** 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 201 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6202 (tp30) REVERT: A 257 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: A 422 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 499 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: A 637 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5723 (m-80) REVERT: A 793 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8491 (mppt) REVERT: B 399 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: B 517 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8548 (tmmm) outliers start: 42 outliers final: 18 residues processed: 183 average time/residue: 0.8624 time to fit residues: 179.2145 Evaluate side-chains 181 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.0925 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= 0.238 Angle : 0.571 7.225 18482 Z= 0.302 Chirality : 0.045 0.180 2095 Planarity : 0.005 0.072 2322 Dihedral : 10.707 179.004 2146 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.65 % Allowed : 17.11 % Favored : 79.24 % Cbeta Deviations : 0.00 % 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: -0.65 (0.20), residues: 1609 helix: 0.75 (0.20), residues: 697 sheet: -1.00 (0.33), residues: 227 loop : -1.43 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.036 0.002 PHE A 789 TYR 0.020 0.002 TYR A 421 ARG 0.003 0.000 ARG A 648 *********************** 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 214 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 163 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6196 (tp30) REVERT: A 250 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6965 (pt0) REVERT: A 499 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 583 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8187 (m110) REVERT: B 270 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: B 399 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: B 507 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7704 (tm-30) outliers start: 51 outliers final: 24 residues processed: 194 average time/residue: 0.8329 time to fit residues: 183.7202 Evaluate side-chains 187 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 253 GLN B 583 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13623 Z= 0.420 Angle : 0.673 10.195 18482 Z= 0.355 Chirality : 0.050 0.216 2095 Planarity : 0.005 0.073 2322 Dihedral : 10.670 179.357 2146 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.44 % Allowed : 17.25 % Favored : 78.31 % Cbeta Deviations : 0.00 % 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: -0.67 (0.20), residues: 1609 helix: 0.77 (0.20), residues: 694 sheet: -1.03 (0.32), residues: 230 loop : -1.48 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 299 HIS 0.006 0.001 HIS A 429 PHE 0.034 0.002 PHE A 789 TYR 0.024 0.003 TYR A 421 ARG 0.004 0.000 ARG A 331 *********************** 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 230 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 168 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6349 (tp30) REVERT: A 499 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 583 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8261 (m110) REVERT: B 270 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: B 399 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: B 634 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8215 (m-80) outliers start: 62 outliers final: 39 residues processed: 202 average time/residue: 0.8345 time to fit residues: 191.8653 Evaluate side-chains 207 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 846 PHE Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN B 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1143 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= 0.265 Angle : 0.586 9.178 18482 Z= 0.309 Chirality : 0.046 0.210 2095 Planarity : 0.005 0.066 2322 Dihedral : 10.433 179.709 2146 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.87 % Allowed : 17.25 % Favored : 77.88 % Cbeta Deviations : 0.00 % 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: -0.48 (0.20), residues: 1609 helix: 0.94 (0.20), residues: 699 sheet: -1.02 (0.33), residues: 227 loop : -1.37 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 299 HIS 0.004 0.001 HIS A 429 PHE 0.017 0.002 PHE A 832 TYR 0.020 0.002 TYR A 421 ARG 0.003 0.000 ARG A 648 *********************** 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 235 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 167 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: A 583 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8265 (m110) REVERT: B 399 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: B 507 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: B 841 ILE cc_start: 0.8211 (mt) cc_final: 0.7991 (mt) outliers start: 68 outliers final: 39 residues processed: 210 average time/residue: 0.7675 time to fit residues: 184.7327 Evaluate side-chains 207 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 846 PHE 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: 1.9990 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: 0.6980 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8225 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13623 Z= 0.257 Angle : 0.602 8.752 18482 Z= 0.319 Chirality : 0.049 0.788 2095 Planarity : 0.005 0.065 2322 Dihedral : 10.381 179.571 2146 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.37 % Allowed : 17.90 % Favored : 77.74 % Cbeta Deviations : 0.00 % 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: -0.40 (0.21), residues: 1609 helix: 1.05 (0.20), residues: 698 sheet: -0.99 (0.33), residues: 227 loop : -1.38 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 299 HIS 0.006 0.001 HIS A 595 PHE 0.017 0.001 PHE A 656 TYR 0.020 0.002 TYR A 421 ARG 0.004 0.000 ARG A 648 *********************** 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 228 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 167 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6910 (pt0) REVERT: A 398 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: A 499 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: A 583 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8258 (m110) REVERT: A 794 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8208 (p) REVERT: B 270 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: B 399 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 507 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: B 841 ILE cc_start: 0.8207 (mt) cc_final: 0.7983 (mt) outliers start: 61 outliers final: 38 residues processed: 203 average time/residue: 0.8141 time to fit residues: 188.9350 Evaluate side-chains 212 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 846 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN B 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1291 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= 0.211 Angle : 0.589 9.741 18482 Z= 0.305 Chirality : 0.050 1.054 2095 Planarity : 0.004 0.063 2322 Dihedral : 10.331 179.806 2146 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.94 % Allowed : 18.97 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.15 (0.20), residues: 700 sheet: -1.02 (0.33), residues: 233 loop : -1.34 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 299 HIS 0.010 0.001 HIS A 595 PHE 0.017 0.001 PHE A 656 TYR 0.017 0.002 TYR A 421 ARG 0.004 0.000 ARG A 648 *********************** 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 223 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 168 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6901 (pt0) REVERT: A 422 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8316 (mp) REVERT: A 499 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: A 583 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8195 (m110) REVERT: A 794 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8311 (p) REVERT: B 270 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: B 399 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: B 507 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: B 841 ILE cc_start: 0.8174 (mt) cc_final: 0.7947 (mt) outliers start: 55 outliers final: 31 residues processed: 200 average time/residue: 0.7838 time to fit residues: 179.6254 Evaluate side-chains 202 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 675 TRP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 846 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13623 Z= 0.199 Angle : 0.569 9.284 18482 Z= 0.293 Chirality : 0.047 0.705 2095 Planarity : 0.004 0.061 2322 Dihedral : 10.361 179.750 2146 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.44 % Allowed : 19.18 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.21 (0.21), residues: 1609 helix: 1.23 (0.20), residues: 705 sheet: -0.91 (0.33), residues: 227 loop : -1.33 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 299 HIS 0.009 0.001 HIS A 595 PHE 0.018 0.001 PHE A 788 TYR 0.018 0.002 TYR A 421 ARG 0.001 0.000 ARG B 69 *********************** 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 210 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 162 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6917 (pt0) REVERT: A 398 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: A 422 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 499 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: A 583 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8126 (m110) REVERT: A 794 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 270 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: B 399 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 507 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: B 517 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8390 (ttmm) REVERT: B 695 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 841 ILE cc_start: 0.8161 (mt) cc_final: 0.7921 (mt) outliers start: 48 outliers final: 28 residues processed: 194 average time/residue: 0.7972 time to fit residues: 176.4600 Evaluate side-chains 198 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 846 PHE 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: 3.9990 chunk 145 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 144 optimal weight: 0.0870 chunk 95 optimal weight: 0.1980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13623 Z= 0.185 Angle : 0.562 9.124 18482 Z= 0.289 Chirality : 0.046 0.472 2095 Planarity : 0.004 0.060 2322 Dihedral : 10.334 179.810 2146 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.86 % Allowed : 19.90 % Favored : 77.24 % Cbeta Deviations : 0.00 % 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: -0.15 (0.21), residues: 1609 helix: 1.28 (0.20), residues: 705 sheet: -0.88 (0.34), residues: 227 loop : -1.29 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 299 HIS 0.006 0.001 HIS A 595 PHE 0.017 0.001 PHE A 656 TYR 0.017 0.001 TYR A 421 ARG 0.001 0.000 ARG A 795 *********************** 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 198 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6907 (pt0) REVERT: A 398 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: A 422 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 499 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: A 583 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8122 (m110) REVERT: A 794 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8581 (p) REVERT: B 270 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: B 399 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: B 507 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: B 695 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8165 (mp) REVERT: B 841 ILE cc_start: 0.8157 (mt) cc_final: 0.7917 (mt) outliers start: 40 outliers final: 25 residues processed: 184 average time/residue: 0.8514 time to fit residues: 178.1801 Evaluate side-chains 193 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 846 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1365 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= 0.319 Angle : 0.624 9.167 18482 Z= 0.324 Chirality : 0.048 0.388 2095 Planarity : 0.005 0.068 2322 Dihedral : 10.358 179.954 2146 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.08 % Allowed : 19.61 % Favored : 77.31 % Cbeta Deviations : 0.00 % 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: -0.24 (0.21), residues: 1609 helix: 1.19 (0.20), residues: 705 sheet: -0.96 (0.33), residues: 228 loop : -1.30 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 299 HIS 0.005 0.001 HIS A 429 PHE 0.019 0.002 PHE A 788 TYR 0.021 0.002 TYR A 421 ARG 0.003 0.000 ARG B 205 ********************** REFINEMENT MACRO_CYCLE 10 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 208 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6938 (pt0) REVERT: A 398 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: A 499 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: A 583 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8198 (m110) REVERT: A 794 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8667 (p) REVERT: B 399 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: B 507 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: B 841 ILE cc_start: 0.8180 (mt) cc_final: 0.7940 (mt) outliers start: 43 outliers final: 31 residues processed: 192 average time/residue: 0.8069 time to fit residues: 177.1584 Evaluate side-chains 200 residues out of total 1414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 846 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS B 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087312 restraints weight = 19291.240| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.58 r_work: 0.2964 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13623 Z= 0.242 Angle : 0.591 9.217 18482 Z= 0.306 Chirality : 0.046 0.352 2095 Planarity : 0.004 0.064 2322 Dihedral : 10.286 179.973 2146 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.65 % Allowed : 20.40 % Favored : 76.95 % Cbeta Deviations : 0.00 % 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: -0.22 (0.21), residues: 1609 helix: 1.21 (0.20), residues: 705 sheet: -0.92 (0.33), residues: 227 loop : -1.30 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 299 HIS 0.004 0.001 HIS A 429 PHE 0.018 0.001 PHE A 656 TYR 0.020 0.002 TYR A 421 ARG 0.003 0.000 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4224.75 seconds wall clock time: 75 minutes 27.31 seconds (4527.31 seconds total)