Starting phenix.real_space_refine on Sat Feb 17 06:42:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryr_10058/02_2024/6ryr_10058_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryr_10058/02_2024/6ryr_10058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryr_10058/02_2024/6ryr_10058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryr_10058/02_2024/6ryr_10058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryr_10058/02_2024/6ryr_10058_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ryr_10058/02_2024/6ryr_10058_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 300 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 10325 2.51 5 N 3271 2.21 5 O 3879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "W ASP 446": "OD1" <-> "OD2" Residue "W GLU 450": "OE1" <-> "OE2" Residue "W GLU 460": "OE1" <-> "OE2" Residue "W ASP 465": "OD1" <-> "OD2" Residue "W TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 482": "OE1" <-> "OE2" Residue "W GLU 540": "OE1" <-> "OE2" Residue "W ARG 541": "NH1" <-> "NH2" Residue "W PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 576": "NH1" <-> "NH2" Residue "W ASP 602": "OD1" <-> "OD2" Residue "W PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 607": "OE1" <-> "OE2" Residue "W ARG 611": "NH1" <-> "NH2" Residue "W GLU 620": "OE1" <-> "OE2" Residue "W ASP 633": "OD1" <-> "OD2" Residue "W ASP 646": "OD1" <-> "OD2" Residue "W TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 655": "OE1" <-> "OE2" Residue "W ASP 663": "OD1" <-> "OD2" Residue "W TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 707": "OD1" <-> "OD2" Residue "W GLU 717": "OE1" <-> "OE2" Residue "W GLU 732": "OE1" <-> "OE2" Residue "W ASP 746": "OD1" <-> "OD2" Residue "W ASP 751": "OD1" <-> "OD2" Residue "W GLU 752": "OE1" <-> "OE2" Residue "W TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 795": "OE1" <-> "OE2" Residue "W ASP 800": "OD1" <-> "OD2" Residue "W TYR 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 818": "OE1" <-> "OE2" Residue "W PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 858": "OD1" <-> "OD2" Residue "W PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 910": "OE1" <-> "OE2" Residue "W GLU 911": "OE1" <-> "OE2" Residue "W PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 922": "OE1" <-> "OE2" Residue "W GLU 928": "OE1" <-> "OE2" Residue "W PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 933": "OE1" <-> "OE2" Residue "W GLU 940": "OE1" <-> "OE2" Residue "W ASP 941": "OD1" <-> "OD2" Residue "W GLU 971": "OE1" <-> "OE2" Residue "W ARG 975": "NH1" <-> "NH2" Residue "W GLU 977": "OE1" <-> "OE2" Residue "W TYR 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 1041": "OD1" <-> "OD2" Residue "W ARG 1047": "NH1" <-> "NH2" Residue "W ASP 1084": "OD1" <-> "OD2" Residue "W GLU 1087": "OE1" <-> "OE2" Residue "W GLU 1089": "OE1" <-> "OE2" Residue "W TYR 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1094": "OE1" <-> "OE2" Residue "W ASP 1097": "OD1" <-> "OD2" Residue "W GLU 1107": "OE1" <-> "OE2" Residue "W PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 1153": "OD1" <-> "OD2" Residue "W PHE 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 1159": "NH1" <-> "NH2" Residue "W TYR 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1181": "OE1" <-> "OE2" Residue "W ARG 1183": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17834 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3036 Classifications: {'DNA': 149} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3070 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "W" Number of atoms: 5728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 712, 5714 Unusual residues: {' MG': 1, ' ZN': 2, 'ANP': 1} Classifications: {'peptide': 708, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 30, 'TRANS': 677, None: 4} Not linked: pdbres="UNK W1212 " pdbres="ANP W2001 " Not linked: pdbres="ANP W2001 " pdbres=" MG W2002 " Not linked: pdbres=" MG W2002 " pdbres=" ZN W2003 " Not linked: pdbres=" ZN W2003 " pdbres=" ZN W2004 " Chain breaks: 4 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 12, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Conformer: "B" Number of residues, atoms: 712, 5714 Unusual residues: {' MG': 1, ' ZN': 2, 'ANP': 1} Classifications: {'peptide': 708, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 30, 'TRANS': 677, None: 4} Not linked: pdbres="UNK W1212 " pdbres="ANP W2001 " Not linked: pdbres="ANP W2001 " pdbres=" MG W2002 " Not linked: pdbres=" MG W2002 " pdbres=" ZN W2003 " Not linked: pdbres=" ZN W2003 " pdbres=" ZN W2004 " Chain breaks: 4 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 12, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 bond proxies already assigned to first conformer: 5837 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12168 SG CYS W 452 53.151 106.010 51.790 1.00119.90 S ATOM 12192 SG CYS W 455 56.142 106.266 52.974 1.00121.24 S ATOM 12340 SG CYS W 475 55.878 107.234 49.266 1.00122.47 S ATOM 12254 SG CYS W 464 39.798 107.120 48.607 1.00120.66 S ATOM 12275 SG CYS W 467 40.507 103.969 49.929 1.00120.83 S ATOM 12458 SG CYS W 490 42.907 104.215 47.121 1.00118.60 S ATOM 12482 SG CYS W 493 39.702 104.419 46.627 1.00115.34 S Time building chain proxies: 11.99, per 1000 atoms: 0.67 Number of scatterers: 17834 At special positions: 0 Unit cell: (97.65, 129.15, 154.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 56 16.00 P 300 15.00 Mg 1 11.99 O 3879 8.00 N 3271 7.00 C 10325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.36 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN W2003 " pdb="ZN ZN W2003 " - pdb=" SG CYS W 455 " pdb="ZN ZN W2003 " - pdb=" SG CYS W 475 " pdb="ZN ZN W2003 " - pdb=" SG CYS W 452 " pdb=" ZN W2004 " pdb="ZN ZN W2004 " - pdb=" SG CYS W 467 " pdb="ZN ZN W2004 " - pdb=" SG CYS W 493 " pdb="ZN ZN W2004 " - pdb=" SG CYS W 490 " pdb="ZN ZN W2004 " - pdb=" SG CYS W 464 " Number of angles added : 6 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 5 sheets defined 50.8% alpha, 4.8% beta 110 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 8.61 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.724A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.856A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.929A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.521A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.587A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.555A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 103 through 120 removed outlier: 3.704A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.963A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.839A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.606A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'W' and resid 552 through 554 No H-bonds generated for 'chain 'W' and resid 552 through 554' Processing helix chain 'W' and resid 560 through 565 removed outlier: 3.660A pdb=" N LEU W 565 " --> pdb=" O LEU W 561 " (cutoff:3.500A) Processing helix chain 'W' and resid 568 through 577 Processing helix chain 'W' and resid 593 through 598 Processing helix chain 'W' and resid 603 through 611 removed outlier: 3.679A pdb=" N GLU W 610 " --> pdb=" O ALA W 606 " (cutoff:3.500A) Processing helix chain 'W' and resid 613 through 615 No H-bonds generated for 'chain 'W' and resid 613 through 615' Processing helix chain 'W' and resid 619 through 622 Processing helix chain 'W' and resid 649 through 651 No H-bonds generated for 'chain 'W' and resid 649 through 651' Processing helix chain 'W' and resid 664 through 677 Processing helix chain 'W' and resid 717 through 722 removed outlier: 3.867A pdb=" N ALA W 721 " --> pdb=" O GLU W 717 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR W 722 " --> pdb=" O TYR W 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 717 through 722' Processing helix chain 'W' and resid 728 through 743 removed outlier: 3.812A pdb=" N GLN W 743 " --> pdb=" O PHE W 739 " (cutoff:3.500A) Processing helix chain 'W' and resid 757 through 771 Processing helix chain 'W' and resid 784 through 790 removed outlier: 4.573A pdb=" N ILE W 788 " --> pdb=" O SER W 785 " (cutoff:3.500A) Processing helix chain 'W' and resid 810 through 820 Processing helix chain 'W' and resid 852 through 857 removed outlier: 4.131A pdb=" N THR W 856 " --> pdb=" O TYR W 852 " (cutoff:3.500A) Processing helix chain 'W' and resid 863 through 865 No H-bonds generated for 'chain 'W' and resid 863 through 865' Processing helix chain 'W' and resid 875 through 877 No H-bonds generated for 'chain 'W' and resid 875 through 877' Processing helix chain 'W' and resid 884 through 891 removed outlier: 3.764A pdb=" N GLY W 891 " --> pdb=" O ARG W 887 " (cutoff:3.500A) Processing helix chain 'W' and resid 909 through 919 Processing helix chain 'W' and resid 928 through 930 No H-bonds generated for 'chain 'W' and resid 928 through 930' Processing helix chain 'W' and resid 939 through 949 removed outlier: 4.117A pdb=" N LYS W 944 " --> pdb=" O GLU W 940 " (cutoff:3.500A) Processing helix chain 'W' and resid 980 through 991 removed outlier: 3.651A pdb=" N TYR W 985 " --> pdb=" O MET W 981 " (cutoff:3.500A) Processing helix chain 'W' and resid 994 through 997 No H-bonds generated for 'chain 'W' and resid 994 through 997' Processing helix chain 'W' and resid 1011 through 1020 removed outlier: 4.116A pdb=" N LYS W1016 " --> pdb=" O VAL W1012 " (cutoff:3.500A) Processing helix chain 'W' and resid 1022 through 1024 No H-bonds generated for 'chain 'W' and resid 1022 through 1024' Processing helix chain 'W' and resid 1026 through 1030 Processing helix chain 'W' and resid 1042 through 1047 Processing helix chain 'W' and resid 1050 through 1065 removed outlier: 3.954A pdb=" N LEU W1054 " --> pdb=" O GLY W1050 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN W1061 " --> pdb=" O LYS W1057 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU W1064 " --> pdb=" O LYS W1060 " (cutoff:3.500A) Processing helix chain 'W' and resid 1078 through 1089 Processing helix chain 'W' and resid 1102 through 1112 Processing helix chain 'W' and resid 1151 through 1157 removed outlier: 3.987A pdb=" N ALA W1156 " --> pdb=" O ASN W1152 " (cutoff:3.500A) Processing helix chain 'W' and resid 1180 through 1192 removed outlier: 3.559A pdb=" N MET W1192 " --> pdb=" O ALA W1188 " (cutoff:3.500A) Processing helix chain 'W' and resid 1203 through 1209 removed outlier: 3.633A pdb=" N UNK W1208 " --> pdb=" O UNK W1204 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 507 through 511 removed outlier: 3.525A pdb=" N ILE W 507 " --> pdb=" O PHE W 544 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU W 540 " --> pdb=" O GLY W 511 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL W 545 " --> pdb=" O SER W 556 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER W 556 " --> pdb=" O VAL W 545 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'W' and resid 653 through 655 removed outlier: 3.618A pdb=" N ARG W 626 " --> pdb=" O LYS W 643 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'W' and resid 897 through 900 removed outlier: 6.105A pdb=" N LEU W 870 " --> pdb=" O LEU W 898 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU W 900 " --> pdb=" O LEU W 870 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL W 872 " --> pdb=" O LEU W 900 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER W 851 " --> pdb=" O TYR W 806 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'W' and resid 969 through 976 removed outlier: 7.397A pdb=" N VAL W1169 " --> pdb=" O THR W 970 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU W 972 " --> pdb=" O VAL W1169 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE W1171 " --> pdb=" O LEU W 972 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL W 974 " --> pdb=" O ILE W1171 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG W1173 " --> pdb=" O VAL W 974 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL W 976 " --> pdb=" O ARG W1173 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL W1175 " --> pdb=" O VAL W 976 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'W' and resid 502 through 505 removed outlier: 6.784A pdb=" N LYS W 546 " --> pdb=" O GLN W 503 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 273 hydrogen bonds 546 hydrogen bond angles 0 basepair planarities 110 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 9.50 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4272 1.33 - 1.45: 4895 1.45 - 1.57: 8937 1.57 - 1.69: 599 1.69 - 1.81: 95 Bond restraints: 18798 Sorted by residual: bond pdb=" O3A ANP W2001 " pdb=" PB ANP W2001 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP W2001 " pdb=" PG ANP W2001 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" O5' ANP W2001 " pdb=" PA ANP W2001 " ideal model delta sigma weight residual 1.655 1.581 0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" O3G ANP W2001 " pdb=" PG ANP W2001 " ideal model delta sigma weight residual 1.528 1.581 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" O2B ANP W2001 " pdb=" PB ANP W2001 " ideal model delta sigma weight residual 1.508 1.556 -0.048 2.00e-02 2.50e+03 5.71e+00 ... (remaining 18793 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.64: 2180 106.64 - 113.57: 10075 113.57 - 120.50: 8095 120.50 - 127.43: 5788 127.43 - 134.36: 541 Bond angle restraints: 26679 Sorted by residual: angle pdb=" PB ANP W2001 " pdb=" N3B ANP W2001 " pdb=" PG ANP W2001 " ideal model delta sigma weight residual 126.95 108.48 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" CB LEU W 480 " pdb=" CG LEU W 480 " pdb=" CD1 LEU W 480 " ideal model delta sigma weight residual 110.70 122.03 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O1B ANP W2001 " pdb=" PB ANP W2001 " pdb=" O2B ANP W2001 " ideal model delta sigma weight residual 120.08 109.43 10.65 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CB LEU W 480 " pdb=" CG LEU W 480 " pdb=" CD2 LEU W 480 " ideal model delta sigma weight residual 110.70 120.32 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N3B ANP W2001 " pdb=" PB ANP W2001 " pdb=" O3A ANP W2001 " ideal model delta sigma weight residual 101.56 110.16 -8.60 3.00e+00 1.11e-01 8.22e+00 ... (remaining 26674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 9220 34.91 - 69.82: 1284 69.82 - 104.73: 38 104.73 - 139.64: 0 139.64 - 174.55: 1 Dihedral angle restraints: 10543 sinusoidal: 6280 harmonic: 4263 Sorted by residual: dihedral pdb=" CA LYS W 546 " pdb=" C LYS W 546 " pdb=" N TRP W 547 " pdb=" CA TRP W 547 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 45.45 174.55 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASN W1004 " pdb=" C ASN W1004 " pdb=" N GLN W1005 " pdb=" CA GLN W1005 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 10540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.355: 2974 0.355 - 0.709: 0 0.709 - 1.064: 0 1.064 - 1.419: 0 1.419 - 1.773: 1 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CG LEU W 480 " pdb=" CB LEU W 480 " pdb=" CD1 LEU W 480 " pdb=" CD2 LEU W 480 " both_signs ideal model delta sigma weight residual False -2.59 -0.82 -1.77 2.00e-01 2.50e+01 7.86e+01 chirality pdb=" C3' ANP W2001 " pdb=" C2' ANP W2001 " pdb=" C4' ANP W2001 " pdb=" O3' ANP W2001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE W 661 " pdb=" CA ILE W 661 " pdb=" CG1 ILE W 661 " pdb=" CG2 ILE W 661 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 2972 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN W 477 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO W 478 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO W 478 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO W 478 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -72 " 0.033 2.00e-02 2.50e+03 1.44e-02 5.73e+00 pdb=" N9 DA J -72 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DA J -72 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DA J -72 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA J -72 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA J -72 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA J -72 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA J -72 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J -72 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA J -72 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA J -72 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY W 951 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO W 952 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO W 952 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO W 952 " -0.032 5.00e-02 4.00e+02 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 77 2.49 - 3.10: 11989 3.10 - 3.70: 28194 3.70 - 4.30: 44118 4.30 - 4.90: 67000 Nonbonded interactions: 151378 Sorted by model distance: nonbonded pdb=" OH TYR W 852 " pdb=" O ASP W 873 " model vdw 1.893 2.440 nonbonded pdb=" OD2 ASP A 81 " pdb=" NH2 ARG W 992 " model vdw 2.123 2.520 nonbonded pdb=" O ASN W1037 " pdb=" ND2 ASN W1037 " model vdw 2.148 2.520 nonbonded pdb=" O2G ANP W2001 " pdb="MG MG W2002 " model vdw 2.153 2.170 nonbonded pdb=" O ALA W 938 " pdb=" N GLN W 942 " model vdw 2.169 2.520 ... (remaining 151373 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 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.680 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: 0.020 Extract box with map and model: 7.830 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 63.260 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.004 0.144 18798 Z= 0.220 Angle : 0.668 18.469 26679 Z= 0.380 Chirality : 0.052 1.773 2975 Planarity : 0.004 0.069 2352 Dihedral : 24.039 174.551 7791 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.16 % Allowed : 0.41 % Favored : 99.43 % 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: -0.14 (0.22), residues: 1429 helix: 0.84 (0.19), residues: 781 sheet: -0.45 (0.54), residues: 91 loop : -1.34 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP W 621 HIS 0.008 0.001 HIS F 75 PHE 0.024 0.002 PHE W 885 TYR 0.029 0.002 TYR W 664 ARG 0.019 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.575 Fit side-chains REVERT: B 16 LYS cc_start: 0.5215 (OUTLIER) cc_final: 0.4692 (ptpp) REVERT: C 36 LYS cc_start: 0.8277 (mmtm) cc_final: 0.8052 (mptt) REVERT: W 622 MET cc_start: 0.8273 (mmm) cc_final: 0.7811 (mmm) REVERT: W 1091 TYR cc_start: 0.7849 (m-10) cc_final: 0.7563 (m-10) REVERT: W 1193 MET cc_start: 0.6195 (mmt) cc_final: 0.5846 (ptt) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.3701 time to fit residues: 95.3044 Evaluate side-chains 161 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS D 44 GLN D 81 ASN E 39 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN H 106 HIS ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 573 ASN W 914 HIS W 998 ASN W1037 ASN W1151 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18798 Z= 0.192 Angle : 0.593 10.488 26679 Z= 0.339 Chirality : 0.038 0.189 2975 Planarity : 0.004 0.052 2352 Dihedral : 27.733 177.596 4908 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.38 % Allowed : 7.81 % Favored : 90.81 % 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: 0.45 (0.22), residues: 1429 helix: 1.33 (0.19), residues: 782 sheet: -0.19 (0.60), residues: 81 loop : -1.08 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP W 621 HIS 0.005 0.001 HIS F 75 PHE 0.021 0.002 PHE W 913 TYR 0.019 0.002 TYR W 574 ARG 0.006 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.614 Fit side-chains REVERT: B 16 LYS cc_start: 0.5078 (OUTLIER) cc_final: 0.4521 (ptpt) REVERT: W 623 MET cc_start: 0.7333 (ptm) cc_final: 0.7063 (ptp) REVERT: W 1091 TYR cc_start: 0.7837 (m-10) cc_final: 0.7524 (m-10) REVERT: W 1193 MET cc_start: 0.6224 (mmt) cc_final: 0.5868 (ptt) outliers start: 17 outliers final: 8 residues processed: 164 average time/residue: 0.3399 time to fit residues: 82.0460 Evaluate side-chains 151 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain W residue 510 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 0.0270 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS B 64 ASN D 44 GLN H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1037 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18798 Z= 0.166 Angle : 0.524 10.043 26679 Z= 0.303 Chirality : 0.035 0.156 2975 Planarity : 0.004 0.049 2352 Dihedral : 27.536 176.606 4908 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.98 % Allowed : 10.74 % Favored : 88.28 % 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: 0.77 (0.22), residues: 1429 helix: 1.65 (0.19), residues: 783 sheet: -0.13 (0.60), residues: 81 loop : -1.03 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 621 HIS 0.003 0.001 HIS F 75 PHE 0.017 0.001 PHE W 913 TYR 0.019 0.001 TYR F 88 ARG 0.008 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 1.678 Fit side-chains REVERT: B 16 LYS cc_start: 0.5327 (OUTLIER) cc_final: 0.4497 (ptpt) REVERT: W 623 MET cc_start: 0.7231 (ptm) cc_final: 0.6748 (ptp) REVERT: W 775 LYS cc_start: 0.7096 (ptpt) cc_final: 0.6856 (ptpp) REVERT: W 1091 TYR cc_start: 0.7717 (m-10) cc_final: 0.7413 (m-10) REVERT: W 1193 MET cc_start: 0.6194 (mmt) cc_final: 0.5819 (ptt) outliers start: 12 outliers final: 7 residues processed: 161 average time/residue: 0.3399 time to fit residues: 80.7958 Evaluate side-chains 153 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 950 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 103 optimal weight: 0.0370 chunk 155 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 overall best weight: 1.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 669 GLN W 715 GLN ** W 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1037 ASN W1155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18798 Z= 0.248 Angle : 0.554 9.895 26679 Z= 0.318 Chirality : 0.037 0.169 2975 Planarity : 0.004 0.070 2352 Dihedral : 27.935 175.344 4908 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.28 % Allowed : 11.31 % Favored : 86.41 % 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: 0.71 (0.22), residues: 1429 helix: 1.63 (0.19), residues: 780 sheet: -0.32 (0.53), residues: 102 loop : -1.08 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 672 HIS 0.003 0.001 HIS W 474 PHE 0.017 0.002 PHE W 886 TYR 0.017 0.001 TYR H 39 ARG 0.009 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.718 Fit side-chains REVERT: B 16 LYS cc_start: 0.5357 (OUTLIER) cc_final: 0.4598 (ptpt) REVERT: D 90 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: W 1030 MET cc_start: 0.7818 (tpp) cc_final: 0.7429 (mmp) REVERT: W 1078 MET cc_start: 0.8335 (tpt) cc_final: 0.8006 (tpt) REVERT: W 1193 MET cc_start: 0.6303 (mmt) cc_final: 0.5914 (ptt) outliers start: 28 outliers final: 9 residues processed: 166 average time/residue: 0.3578 time to fit residues: 86.7278 Evaluate side-chains 154 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 811 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 44 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 876 HIS ** W 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1037 ASN W1155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18798 Z= 0.267 Angle : 0.554 10.785 26679 Z= 0.317 Chirality : 0.037 0.156 2975 Planarity : 0.004 0.077 2352 Dihedral : 28.060 177.524 4908 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.95 % Allowed : 12.53 % Favored : 85.52 % 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 (0.22), residues: 1429 helix: 1.59 (0.19), residues: 780 sheet: -0.10 (0.58), residues: 87 loop : -1.15 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 488 HIS 0.003 0.001 HIS E 39 PHE 0.017 0.002 PHE W 913 TYR 0.019 0.001 TYR H 39 ARG 0.013 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.608 Fit side-chains REVERT: B 16 LYS cc_start: 0.5292 (OUTLIER) cc_final: 0.4581 (ptpp) REVERT: D 30 ARG cc_start: 0.7599 (tpp80) cc_final: 0.6711 (tmt170) REVERT: D 56 MET cc_start: 0.8209 (tpt) cc_final: 0.7376 (tpt) REVERT: D 90 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: G 113 SER cc_start: 0.8534 (p) cc_final: 0.8332 (m) REVERT: W 1193 MET cc_start: 0.6290 (mmt) cc_final: 0.5952 (ptt) outliers start: 24 outliers final: 12 residues processed: 157 average time/residue: 0.3656 time to fit residues: 83.6919 Evaluate side-chains 153 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 872 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18798 Z= 0.375 Angle : 0.606 10.208 26679 Z= 0.343 Chirality : 0.040 0.170 2975 Planarity : 0.005 0.081 2352 Dihedral : 28.501 174.534 4908 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.12 % Allowed : 13.75 % Favored : 84.13 % 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: 0.35 (0.22), residues: 1429 helix: 1.38 (0.19), residues: 775 sheet: -0.36 (0.53), residues: 102 loop : -1.32 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP W 488 HIS 0.004 0.001 HIS W 876 PHE 0.017 0.002 PHE W 886 TYR 0.024 0.002 TYR H 39 ARG 0.012 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.623 Fit side-chains REVERT: A 42 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6844 (mtm-85) REVERT: B 16 LYS cc_start: 0.5272 (OUTLIER) cc_final: 0.4682 (ptpt) REVERT: D 30 ARG cc_start: 0.7775 (tpp80) cc_final: 0.6949 (tmt170) REVERT: D 90 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: W 1078 MET cc_start: 0.8390 (tpt) cc_final: 0.8025 (tpt) REVERT: W 1192 MET cc_start: 0.7934 (ptm) cc_final: 0.7633 (ptm) REVERT: W 1193 MET cc_start: 0.6405 (mmt) cc_final: 0.6087 (ptt) outliers start: 26 outliers final: 17 residues processed: 155 average time/residue: 0.3640 time to fit residues: 81.2657 Evaluate side-chains 158 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 908 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 102 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18798 Z= 0.265 Angle : 0.569 10.660 26679 Z= 0.327 Chirality : 0.038 0.192 2975 Planarity : 0.005 0.076 2352 Dihedral : 28.454 174.917 4908 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.28 % Allowed : 14.08 % Favored : 83.65 % 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: 0.43 (0.22), residues: 1429 helix: 1.45 (0.19), residues: 776 sheet: -0.31 (0.53), residues: 102 loop : -1.32 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 488 HIS 0.005 0.001 HIS W 876 PHE 0.017 0.002 PHE W 913 TYR 0.021 0.002 TYR H 39 ARG 0.009 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.583 Fit side-chains REVERT: A 42 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6787 (mtm-85) REVERT: B 16 LYS cc_start: 0.5267 (OUTLIER) cc_final: 0.4667 (ptpt) REVERT: D 30 ARG cc_start: 0.7714 (tpp80) cc_final: 0.6885 (tmt170) REVERT: D 90 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: W 981 MET cc_start: 0.7976 (tmm) cc_final: 0.7740 (tmm) REVERT: W 1192 MET cc_start: 0.7956 (ptm) cc_final: 0.7645 (ptm) REVERT: W 1193 MET cc_start: 0.6374 (mmt) cc_final: 0.6049 (ptt) outliers start: 28 outliers final: 21 residues processed: 158 average time/residue: 0.3455 time to fit residues: 79.1453 Evaluate side-chains 159 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 908 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18798 Z= 0.250 Angle : 0.560 10.752 26679 Z= 0.321 Chirality : 0.037 0.165 2975 Planarity : 0.004 0.076 2352 Dihedral : 28.388 175.383 4908 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.28 % Allowed : 14.65 % Favored : 83.08 % 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: 0.50 (0.22), residues: 1429 helix: 1.52 (0.19), residues: 776 sheet: -0.33 (0.53), residues: 102 loop : -1.29 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 553 HIS 0.003 0.001 HIS W 876 PHE 0.016 0.002 PHE W 913 TYR 0.020 0.001 TYR H 39 ARG 0.007 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.622 Fit side-chains REVERT: A 42 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6787 (mtm-85) REVERT: B 16 LYS cc_start: 0.5259 (OUTLIER) cc_final: 0.4666 (ptpt) REVERT: D 30 ARG cc_start: 0.7709 (tpp80) cc_final: 0.6875 (tmt170) REVERT: D 90 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: F 84 MET cc_start: 0.7405 (mmm) cc_final: 0.6874 (mmm) REVERT: W 623 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6983 (pmm) REVERT: W 1192 MET cc_start: 0.7923 (ptm) cc_final: 0.7608 (ptm) REVERT: W 1193 MET cc_start: 0.6364 (mmt) cc_final: 0.6038 (ptt) outliers start: 28 outliers final: 22 residues processed: 152 average time/residue: 0.3419 time to fit residues: 76.2083 Evaluate side-chains 161 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 623 MET Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 908 ASN Chi-restraints excluded: chain W residue 1166 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.0870 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 0.0070 chunk 161 optimal weight: 3.9990 overall best weight: 1.0338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18798 Z= 0.189 Angle : 0.543 12.071 26679 Z= 0.313 Chirality : 0.036 0.166 2975 Planarity : 0.004 0.071 2352 Dihedral : 28.337 175.681 4908 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.03 % Allowed : 14.97 % Favored : 82.99 % 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 (0.22), residues: 1429 helix: 1.66 (0.19), residues: 776 sheet: -0.32 (0.53), residues: 102 loop : -1.23 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 488 HIS 0.003 0.001 HIS E 39 PHE 0.016 0.001 PHE W 913 TYR 0.019 0.001 TYR H 39 ARG 0.006 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.590 Fit side-chains REVERT: A 42 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6785 (mtm-85) REVERT: B 16 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.4711 (ptpt) REVERT: D 30 ARG cc_start: 0.7699 (tpp80) cc_final: 0.6862 (tmt170) REVERT: F 84 MET cc_start: 0.7414 (mmm) cc_final: 0.6887 (mmm) REVERT: H 56 MET cc_start: 0.8338 (tpp) cc_final: 0.8104 (tpp) REVERT: W 623 MET cc_start: 0.7723 (pmm) cc_final: 0.7263 (pmm) REVERT: W 1192 MET cc_start: 0.7877 (ptm) cc_final: 0.7552 (ptm) REVERT: W 1193 MET cc_start: 0.6344 (mmt) cc_final: 0.6016 (ptt) outliers start: 25 outliers final: 19 residues processed: 154 average time/residue: 0.3534 time to fit residues: 80.6892 Evaluate side-chains 154 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 803 VAL Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 908 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 18798 Z= 0.346 Angle : 0.586 10.955 26679 Z= 0.334 Chirality : 0.039 0.168 2975 Planarity : 0.005 0.082 2352 Dihedral : 28.438 175.667 4908 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.20 % Allowed : 15.05 % Favored : 82.75 % 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: 0.41 (0.22), residues: 1429 helix: 1.45 (0.19), residues: 774 sheet: -0.35 (0.53), residues: 102 loop : -1.32 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 488 HIS 0.005 0.001 HIS W 876 PHE 0.017 0.002 PHE W 886 TYR 0.022 0.002 TYR H 39 ARG 0.008 0.001 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.748 Fit side-chains REVERT: A 42 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6872 (mtm-85) REVERT: B 16 LYS cc_start: 0.5336 (OUTLIER) cc_final: 0.4737 (ptpt) REVERT: D 30 ARG cc_start: 0.7701 (tpp80) cc_final: 0.6908 (tmt170) REVERT: F 84 MET cc_start: 0.7455 (mmm) cc_final: 0.6910 (mmm) REVERT: W 623 MET cc_start: 0.7716 (pmm) cc_final: 0.7205 (pmm) REVERT: W 1192 MET cc_start: 0.7947 (ptm) cc_final: 0.7639 (ptm) REVERT: W 1193 MET cc_start: 0.6383 (mmt) cc_final: 0.6065 (ptt) outliers start: 27 outliers final: 23 residues processed: 156 average time/residue: 0.3459 time to fit residues: 78.7098 Evaluate side-chains 161 residues out of total 1246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 570 MET Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 803 VAL Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 908 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 998 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105647 restraints weight = 30793.392| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.27 r_work: 0.3223 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18798 Z= 0.174 Angle : 0.554 12.100 26679 Z= 0.319 Chirality : 0.037 0.227 2975 Planarity : 0.004 0.074 2352 Dihedral : 28.389 175.981 4908 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.63 % Allowed : 15.62 % Favored : 82.75 % 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: 0.66 (0.22), residues: 1429 helix: 1.66 (0.19), residues: 780 sheet: -0.38 (0.52), residues: 102 loop : -1.23 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 547 HIS 0.004 0.001 HIS E 39 PHE 0.018 0.001 PHE W 667 TYR 0.021 0.001 TYR H 39 ARG 0.005 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3379.84 seconds wall clock time: 62 minutes 10.27 seconds (3730.27 seconds total)