Starting phenix.real_space_refine on Sun Aug 9 05:13:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30yx_58157/08_2026/30yx_58157.cif Found real_map, /net/cci-nas-00/data/ceres_data/30yx_58157/08_2026/30yx_58157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30yx_58157/08_2026/30yx_58157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30yx_58157/08_2026/30yx_58157.map" model { file = "/net/cci-nas-00/data/ceres_data/30yx_58157/08_2026/30yx_58157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30yx_58157/08_2026/30yx_58157.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.042 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 60 5.16 5 C 20320 2.51 5 N 5234 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32111 Number of models: 1 Model: "" Number of chains: 27 Chain: "Y" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1465 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "a" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1465 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "b" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1465 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "c" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1465 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "d" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1465 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "A" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Chain: "M" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2763 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 8, 'TRANS': 342} Chain: "N" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2763 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "O" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2763 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "B" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Chain: "C" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Chain: "D" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Chain: "E" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Chain: "F" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 407 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 235 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 235 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 407 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 407 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "Z" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1465 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.40, per 1000 atoms: 0.23 Number of scatterers: 32111 At special positions: 0 Unit cell: (150.181, 159.41, 154.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 60 16.00 O 6491 8.00 N 5234 7.00 C 20320 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 - 3.00 Amino acid : True - 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: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7668 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 53 sheets defined 16.8% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'Y' and resid 84 through 93 Processing helix chain 'Y' and resid 162 through 166 Processing helix chain 'Y' and resid 181 through 190 Processing helix chain 'a' and resid 84 through 93 Processing helix chain 'a' and resid 162 through 166 Processing helix chain 'a' and resid 181 through 190 Processing helix chain 'b' and resid 59 through 63 removed outlier: 3.924A pdb=" N ASN b 62 " --> pdb=" O TYR b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 93 Processing helix chain 'b' and resid 162 through 166 Processing helix chain 'b' and resid 181 through 190 Processing helix chain 'c' and resid 84 through 93 Processing helix chain 'c' and resid 162 through 166 Processing helix chain 'c' and resid 181 through 190 Processing helix chain 'd' and resid 59 through 63 removed outlier: 3.987A pdb=" N ASN d 62 " --> pdb=" O TYR d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 93 Processing helix chain 'd' and resid 162 through 166 Processing helix chain 'd' and resid 181 through 190 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.897A pdb=" N GLN A 603 " --> pdb=" O PRO A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'M' and resid 89 through 93 Processing helix chain 'M' and resid 105 through 118 Processing helix chain 'M' and resid 119 through 121 No H-bonds generated for 'chain 'M' and resid 119 through 121' Processing helix chain 'M' and resid 151 through 163 Processing helix chain 'M' and resid 277 through 287 Processing helix chain 'M' and resid 307 through 311 Processing helix chain 'N' and resid 89 through 93 Processing helix chain 'N' and resid 105 through 118 Processing helix chain 'N' and resid 119 through 121 No H-bonds generated for 'chain 'N' and resid 119 through 121' Processing helix chain 'N' and resid 124 through 128 removed outlier: 4.123A pdb=" N HIS N 128 " --> pdb=" O ILE N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 163 Processing helix chain 'N' and resid 277 through 287 Processing helix chain 'N' and resid 307 through 311 Processing helix chain 'O' and resid 89 through 93 Processing helix chain 'O' and resid 105 through 119 Processing helix chain 'O' and resid 150 through 163 Processing helix chain 'O' and resid 277 through 287 Processing helix chain 'O' and resid 307 through 311 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 618 through 621 Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 618 through 621 removed outlier: 3.775A pdb=" N GLN D 621 " --> pdb=" O SER D 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 621' Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 69 through 82 Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.954A pdb=" N GLN E 603 " --> pdb=" O PRO E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 621 Processing helix chain 'F' and resid 66 through 68 No H-bonds generated for 'chain 'F' and resid 66 through 68' Processing helix chain 'F' and resid 69 through 82 Processing helix chain 'F' and resid 599 through 603 removed outlier: 3.888A pdb=" N GLN F 603 " --> pdb=" O PRO F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 621 Processing helix chain 'G' and resid 1558 through 1579 removed outlier: 4.106A pdb=" N ASN G1567 " --> pdb=" O LEU G1563 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL G1573 " --> pdb=" O GLN G1569 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU G1574 " --> pdb=" O LEU G1570 " (cutoff:3.500A) Processing helix chain 'G' and resid 1580 through 1587 removed outlier: 3.681A pdb=" N GLU G1584 " --> pdb=" O SER G1580 " (cutoff:3.500A) Processing helix chain 'G' and resid 1593 through 1611 Processing helix chain 'H' and resid 1558 through 1585 Processing helix chain 'I' and resid 1558 through 1587 removed outlier: 3.734A pdb=" N GLY I1565 " --> pdb=" O GLU I1561 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN I1566 " --> pdb=" O THR I1562 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU I1582 " --> pdb=" O VAL I1578 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY I1583 " --> pdb=" O GLY I1579 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU I1584 " --> pdb=" O SER I1580 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL I1585 " --> pdb=" O ILE I1581 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS I1586 " --> pdb=" O LEU I1582 " (cutoff:3.500A) Processing helix chain 'J' and resid 1558 through 1587 removed outlier: 4.873A pdb=" N SER J1580 " --> pdb=" O ASN J1576 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE J1581 " --> pdb=" O VAL J1577 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU J1582 " --> pdb=" O VAL J1578 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY J1583 " --> pdb=" O GLY J1579 " (cutoff:3.500A) Processing helix chain 'J' and resid 1593 through 1611 Processing helix chain 'K' and resid 1558 through 1579 removed outlier: 3.753A pdb=" N ASN K1567 " --> pdb=" O LEU K1563 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL K1573 " --> pdb=" O GLN K1569 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU K1574 " --> pdb=" O LEU K1570 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY K1579 " --> pdb=" O THR K1575 " (cutoff:3.500A) Processing helix chain 'K' and resid 1579 through 1590 removed outlier: 4.368A pdb=" N GLY K1583 " --> pdb=" O GLY K1579 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY K1588 " --> pdb=" O GLU K1584 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN K1590 " --> pdb=" O LYS K1586 " (cutoff:3.500A) Processing helix chain 'K' and resid 1593 through 1611 Processing helix chain 'L' and resid 1558 through 1563 Processing helix chain 'L' and resid 1566 through 1580 removed outlier: 3.689A pdb=" N LEU L1570 " --> pdb=" O GLN L1566 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU L1574 " --> pdb=" O LEU L1570 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR L1575 " --> pdb=" O ILE L1571 " (cutoff:3.500A) Processing helix chain 'L' and resid 1581 through 1589 removed outlier: 3.840A pdb=" N VAL L1585 " --> pdb=" O LEU L1582 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS L1586 " --> pdb=" O GLY L1583 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA L1587 " --> pdb=" O GLU L1584 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 63 removed outlier: 3.944A pdb=" N ASN Z 62 " --> pdb=" O TYR Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 93 Processing helix chain 'Z' and resid 162 through 166 Processing helix chain 'Z' and resid 181 through 190 Processing sheet with id=AA1, first strand: chain 'Y' and resid 3 through 14 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 33 through 35 current: chain 'Y' and resid 124 through 129 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 170 through 174 current: chain 'Z' and resid 101 through 104 Processing sheet with id=AA2, first strand: chain 'Y' and resid 132 through 135 removed outlier: 6.653A pdb=" N SER Y 75 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE Y 48 " --> pdb=" O SER Y 75 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA Y 77 " --> pdb=" O ALA Y 46 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA Y 46 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP Y 79 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER Y 42 " --> pdb=" O ASN Y 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 56 through 59 removed outlier: 3.573A pdb=" N ASP Y 66 " --> pdb=" O VAL Y 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 94 through 96 removed outlier: 5.541A pdb=" N GLN Y 104 " --> pdb=" O GLY d 170 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N GLY d 170 " --> pdb=" O GLN Y 104 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS d 109 " --> pdb=" O VAL d 14 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU d 8 " --> pdb=" O THR d 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 150 through 151 removed outlier: 3.534A pdb=" N THR d 3 " --> pdb=" O ASN Y 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 3 through 14 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 33 through 35 current: chain 'a' and resid 124 through 129 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 170 through 174 current: chain 'b' and resid 101 through 104 Processing sheet with id=AA7, first strand: chain 'a' and resid 132 through 135 removed outlier: 3.630A pdb=" N ASP a 153 " --> pdb=" O PHE a 80 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE a 80 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER a 75 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE a 48 " --> pdb=" O SER a 75 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA a 77 " --> pdb=" O ALA a 46 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA a 46 " --> pdb=" O ALA a 77 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP a 79 " --> pdb=" O LYS a 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER a 42 " --> pdb=" O ASN a 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 56 through 57 Processing sheet with id=AA9, first strand: chain 'a' and resid 94 through 96 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 101 through 104 current: chain 'Z' and resid 3 through 14 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 33 through 35 current: chain 'Z' and resid 124 through 129 Processing sheet with id=AB1, first strand: chain 'b' and resid 3 through 14 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 33 through 35 current: chain 'b' and resid 124 through 129 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 170 through 174 current: chain 'c' and resid 101 through 104 Processing sheet with id=AB2, first strand: chain 'b' and resid 42 through 49 removed outlier: 6.455A pdb=" N SER b 42 " --> pdb=" O ASN b 81 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP b 79 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA b 46 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA b 77 " --> pdb=" O ALA b 46 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE b 48 " --> pdb=" O SER b 75 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER b 75 " --> pdb=" O ILE b 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 56 through 57 Processing sheet with id=AB4, first strand: chain 'c' and resid 33 through 35 removed outlier: 7.203A pdb=" N LEU c 6 " --> pdb=" O ASP c 117 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP c 117 " --> pdb=" O LEU c 6 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS c 109 " --> pdb=" O VAL c 14 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N GLY c 170 " --> pdb=" O GLN d 104 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLN d 104 " --> pdb=" O GLY c 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 132 through 135 removed outlier: 6.749A pdb=" N SER c 75 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE c 48 " --> pdb=" O SER c 75 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA c 77 " --> pdb=" O ALA c 46 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA c 46 " --> pdb=" O ALA c 77 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP c 79 " --> pdb=" O LYS c 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 56 through 59 removed outlier: 3.893A pdb=" N ASP c 66 " --> pdb=" O VAL c 58 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 42 through 49 removed outlier: 6.547A pdb=" N SER d 42 " --> pdb=" O ASN d 81 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP d 79 " --> pdb=" O LYS d 44 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA d 46 " --> pdb=" O ALA d 77 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA d 77 " --> pdb=" O ALA d 46 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE d 48 " --> pdb=" O SER d 75 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER d 75 " --> pdb=" O ILE d 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 56 through 57 Processing sheet with id=AB9, first strand: chain 'A' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 11 through 13 current: chain 'A' and resid 57 through 63 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 57 through 63 current: chain 'A' and resid 96 through 106 removed outlier: 6.984A pdb=" N ILE A 127 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 106 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 125 " --> pdb=" O ILE A 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 122 through 130 current: chain 'C' and resid 42 through 49 Processing sheet with id=AC1, first strand: chain 'A' and resid 29 through 37 removed outlier: 6.729A pdb=" N SER A 36 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS A 44 " --> pdb=" O SER A 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 42 through 49 current: chain 'B' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 11 through 13 current: chain 'B' and resid 57 through 63 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 57 through 63 current: chain 'B' and resid 95 through 106 removed outlier: 6.960A pdb=" N ILE B 127 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE B 106 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA B 125 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 134 through 141 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 134 through 141 current: chain 'A' and resid 593 through 597 Processing sheet with id=AC3, first strand: chain 'A' and resid 537 through 543 removed outlier: 3.846A pdb=" N ALA A 580 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN A 574 " --> pdb=" O THR A 578 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N THR A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 5 through 10 removed outlier: 4.938A pdb=" N LEU M 5 " --> pdb=" O VAL M 22 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY M 18 " --> pdb=" O ILE M 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 16 through 25 current: chain 'M' and resid 63 through 75 removed outlier: 5.495A pdb=" N LEU M 69 " --> pdb=" O ASN M 86 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN M 86 " --> pdb=" O LEU M 69 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 82 through 87 current: chain 'M' and resid 293 through 300 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 293 through 300 current: chain 'M' and resid 341 through 346 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 341 through 346 current: chain 'N' and resid 16 through 30 removed outlier: 4.143A pdb=" N THR N 38 " --> pdb=" O SER N 26 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 37 through 41 current: chain 'N' and resid 63 through 75 removed outlier: 6.909A pdb=" N THR N 84 " --> pdb=" O THR N 70 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL N 72 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR N 82 " --> pdb=" O VAL N 72 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 82 through 87 current: chain 'N' and resid 293 through 300 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 293 through 300 current: chain 'N' and resid 324 through 336 removed outlier: 4.790A pdb=" N THR N 336 " --> pdb=" O LEU N 341 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU N 341 " --> pdb=" O THR N 336 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 341 through 346 current: chain 'O' and resid 16 through 30 removed outlier: 6.662A pdb=" N VAL O 40 " --> pdb=" O LEU O 23 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR O 25 " --> pdb=" O THR O 38 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR O 38 " --> pdb=" O TYR O 25 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 37 through 41 current: chain 'O' and resid 63 through 75 removed outlier: 6.905A pdb=" N THR O 84 " --> pdb=" O THR O 70 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL O 72 " --> pdb=" O THR O 82 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR O 82 " --> pdb=" O VAL O 72 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 82 through 87 current: chain 'O' and resid 293 through 300 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 293 through 300 current: chain 'O' and resid 324 through 336 removed outlier: 6.508A pdb=" N LEU O 330 " --> pdb=" O GLY O 347 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY O 347 " --> pdb=" O LEU O 330 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR O 336 " --> pdb=" O LEU O 341 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU O 341 " --> pdb=" O THR O 336 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 95 through 98 Processing sheet with id=AC6, first strand: chain 'M' and resid 101 through 103 Processing sheet with id=AC7, first strand: chain 'M' and resid 130 through 132 removed outlier: 6.465A pdb=" N THR M 131 " --> pdb=" O ILE M 188 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLN M 190 " --> pdb=" O THR M 131 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP M 170 " --> pdb=" O GLU M 185 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP M 187 " --> pdb=" O ILE M 168 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE M 168 " --> pdb=" O ASP M 187 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS M 189 " --> pdb=" O ILE M 166 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE M 166 " --> pdb=" O HIS M 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 194 through 198 Processing sheet with id=AC9, first strand: chain 'M' and resid 249 through 250 removed outlier: 7.544A pdb=" N ILE M 237 " --> pdb=" O ASP M 226 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASP M 226 " --> pdb=" O ILE M 237 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA M 239 " --> pdb=" O ILE M 224 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TYR M 266 " --> pdb=" O GLU M 221 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TRP M 223 " --> pdb=" O TYR M 266 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR M 268 " --> pdb=" O TRP M 223 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL M 225 " --> pdb=" O TYR M 268 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 95 through 98 Processing sheet with id=AD2, first strand: chain 'N' and resid 101 through 103 Processing sheet with id=AD3, first strand: chain 'N' and resid 130 through 132 removed outlier: 6.620A pdb=" N THR N 131 " --> pdb=" O ILE N 188 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N GLN N 190 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP N 170 " --> pdb=" O GLU N 185 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP N 187 " --> pdb=" O ILE N 168 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE N 168 " --> pdb=" O ASP N 187 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N HIS N 189 " --> pdb=" O ILE N 166 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE N 166 " --> pdb=" O HIS N 189 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 249 through 250 removed outlier: 6.895A pdb=" N ILE N 224 " --> pdb=" O ILE N 238 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS N 240 " --> pdb=" O LEU N 222 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU N 222 " --> pdb=" O LYS N 240 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N TYR N 266 " --> pdb=" O GLU N 221 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TRP N 223 " --> pdb=" O TYR N 266 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR N 268 " --> pdb=" O TRP N 223 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL N 225 " --> pdb=" O TYR N 268 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 96 through 98 Processing sheet with id=AD6, first strand: chain 'O' and resid 130 through 132 removed outlier: 6.609A pdb=" N THR O 131 " --> pdb=" O ILE O 188 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN O 190 " --> pdb=" O THR O 131 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP O 170 " --> pdb=" O GLU O 185 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP O 187 " --> pdb=" O ILE O 168 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE O 168 " --> pdb=" O ASP O 187 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS O 189 " --> pdb=" O ILE O 166 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE O 166 " --> pdb=" O HIS O 189 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 249 through 250 removed outlier: 6.837A pdb=" N ILE O 224 " --> pdb=" O ILE O 238 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS O 240 " --> pdb=" O LEU O 222 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU O 222 " --> pdb=" O LYS O 240 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU O 221 " --> pdb=" O HIS O 264 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TYR O 266 " --> pdb=" O GLU O 221 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TRP O 223 " --> pdb=" O TYR O 266 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR O 268 " --> pdb=" O TRP O 223 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL O 225 " --> pdb=" O TYR O 268 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 29 through 38 removed outlier: 7.668A pdb=" N THR B 30 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE B 49 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS B 32 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 47 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 34 " --> pdb=" O THR B 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 41 through 49 current: chain 'F' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 11 through 13 current: chain 'F' and resid 57 through 63 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 63 current: chain 'F' and resid 96 through 106 removed outlier: 6.972A pdb=" N ILE F 127 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE F 106 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA F 125 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 134 through 141 Processing sheet with id=AE1, first strand: chain 'B' and resid 536 through 543 removed outlier: 3.676A pdb=" N THR B 637 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B 569 " --> pdb=" O TYR B 641 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 568 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN B 574 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AE3, first strand: chain 'C' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 11 through 13 current: chain 'C' and resid 57 through 63 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 63 current: chain 'C' and resid 95 through 106 removed outlier: 6.952A pdb=" N ILE C 127 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE C 106 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA C 125 " --> pdb=" O ILE C 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 122 through 130 current: chain 'E' and resid 42 through 49 Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 141 Processing sheet with id=AE5, first strand: chain 'C' and resid 536 through 543 removed outlier: 3.995A pdb=" N SER C 569 " --> pdb=" O TYR C 641 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL C 568 " --> pdb=" O ALA C 583 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA C 583 " --> pdb=" O VAL C 568 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TRP C 570 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER C 581 " --> pdb=" O TRP C 570 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C 572 " --> pdb=" O ILE C 579 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AE7, first strand: chain 'D' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 11 through 13 current: chain 'D' and resid 57 through 63 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 63 current: chain 'D' and resid 95 through 106 removed outlier: 6.891A pdb=" N ILE D 127 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE D 106 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA D 125 " --> pdb=" O ILE D 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 122 through 130 current: chain 'F' and resid 42 through 49 Processing sheet with id=AE8, first strand: chain 'D' and resid 29 through 38 removed outlier: 6.752A pdb=" N SER D 36 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LYS D 44 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR D 38 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE D 42 " --> pdb=" O TYR D 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 41 through 49 current: chain 'E' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 11 through 13 current: chain 'E' and resid 57 through 63 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 63 current: chain 'E' and resid 96 through 106 removed outlier: 6.957A pdb=" N ILE E 127 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA E 125 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 134 through 141 Processing sheet with id=AF1, first strand: chain 'D' and resid 536 through 543 removed outlier: 4.104A pdb=" N SER D 569 " --> pdb=" O TYR D 641 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL D 568 " --> pdb=" O ALA D 583 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA D 583 " --> pdb=" O VAL D 568 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP D 570 " --> pdb=" O SER D 581 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER D 581 " --> pdb=" O TRP D 570 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL D 572 " --> pdb=" O ILE D 579 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 553 through 554 Processing sheet with id=AF3, first strand: chain 'E' and resid 134 through 141 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 134 through 141 current: chain 'E' and resid 593 through 597 Processing sheet with id=AF4, first strand: chain 'E' and resid 536 through 543 removed outlier: 4.091A pdb=" N SER E 569 " --> pdb=" O TYR E 641 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA E 580 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN E 574 " --> pdb=" O THR E 578 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR E 578 " --> pdb=" O GLN E 574 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 134 through 141 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 134 through 141 current: chain 'F' and resid 593 through 597 Processing sheet with id=AF6, first strand: chain 'F' and resid 537 through 543 removed outlier: 3.786A pdb=" N ALA F 580 " --> pdb=" O VAL F 572 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN F 574 " --> pdb=" O THR F 578 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR F 578 " --> pdb=" O GLN F 574 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 43 through 49 removed outlier: 6.683A pdb=" N ASP Z 79 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA Z 46 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA Z 77 " --> pdb=" O ALA Z 46 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE Z 48 " --> pdb=" O SER Z 75 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER Z 75 " --> pdb=" O ILE Z 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 56 through 57 901 hydrogen bonds defined for protein. 2409 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: 6.77 Time building geometry restraints manager: 3.55 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: 10472 1.34 - 1.46: 6423 1.46 - 1.57: 15732 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 32741 Sorted by residual: bond pdb=" N ASN L1557 " pdb=" CA ASN L1557 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.52e+00 bond pdb=" N MET d 1 " pdb=" CA MET d 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.24e+00 bond pdb=" N MET Y 1 " pdb=" CA MET Y 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N SER M 2 " pdb=" CA SER M 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N MET a 1 " pdb=" CA MET a 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 32736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 44350 2.10 - 4.20: 262 4.20 - 6.30: 11 6.30 - 8.40: 2 8.40 - 10.50: 1 Bond angle restraints: 44626 Sorted by residual: angle pdb=" CA LEU B 588 " pdb=" CB LEU B 588 " pdb=" CG LEU B 588 " ideal model delta sigma weight residual 116.30 126.80 -10.50 3.50e+00 8.16e-02 8.99e+00 angle pdb=" C ILE O 88 " pdb=" N TRP O 89 " pdb=" CA TRP O 89 " ideal model delta sigma weight residual 121.52 114.74 6.78 2.34e+00 1.83e-01 8.39e+00 angle pdb=" N ILE E 116 " pdb=" CA ILE E 116 " pdb=" C ILE E 116 " ideal model delta sigma weight residual 111.62 109.42 2.20 7.90e-01 1.60e+00 7.72e+00 angle pdb=" C ILE N 88 " pdb=" N TRP N 89 " pdb=" CA TRP N 89 " ideal model delta sigma weight residual 121.52 115.28 6.24 2.34e+00 1.83e-01 7.11e+00 angle pdb=" N TRP N 89 " pdb=" CA TRP N 89 " pdb=" CB TRP N 89 " ideal model delta sigma weight residual 110.42 115.02 -4.60 1.76e+00 3.23e-01 6.83e+00 ... (remaining 44621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 17733 17.72 - 35.43: 1212 35.43 - 53.15: 198 53.15 - 70.86: 62 70.86 - 88.58: 40 Dihedral angle restraints: 19245 sinusoidal: 7215 harmonic: 12030 Sorted by residual: dihedral pdb=" CA TYR M 87 " pdb=" C TYR M 87 " pdb=" N ILE M 88 " pdb=" CA ILE M 88 " ideal model delta harmonic sigma weight residual -180.00 -150.33 -29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA TYR N 87 " pdb=" C TYR N 87 " pdb=" N ILE N 88 " pdb=" CA ILE N 88 " ideal model delta harmonic sigma weight residual 180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLY L1565 " pdb=" C GLY L1565 " pdb=" N GLN L1566 " pdb=" CA GLN L1566 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 19242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3031 0.029 - 0.057: 1451 0.057 - 0.086: 269 0.086 - 0.114: 265 0.114 - 0.143: 141 Chirality restraints: 5157 Sorted by residual: chirality pdb=" CA ILE C 539 " pdb=" N ILE C 539 " pdb=" C ILE C 539 " pdb=" CB ILE C 539 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE O 166 " pdb=" N ILE O 166 " pdb=" C ILE O 166 " pdb=" CB ILE O 166 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE D 539 " pdb=" N ILE D 539 " pdb=" C ILE D 539 " pdb=" CB ILE D 539 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 5154 not shown) Planarity restraints: 5759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 89 " -0.026 2.00e-02 2.50e+03 2.31e-02 1.34e+01 pdb=" CG TRP N 89 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP N 89 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP N 89 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP N 89 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP N 89 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP N 89 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 89 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 89 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP N 89 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 89 " -0.027 2.00e-02 2.50e+03 2.20e-02 1.22e+01 pdb=" CG TRP O 89 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP O 89 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP O 89 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP O 89 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 89 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP O 89 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 89 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 89 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP O 89 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 89 " 0.012 2.00e-02 2.50e+03 9.54e-03 2.28e+00 pdb=" CG TRP M 89 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP M 89 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP M 89 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP M 89 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP M 89 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M 89 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 89 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 89 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP M 89 " -0.000 2.00e-02 2.50e+03 ... (remaining 5756 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 280 2.59 - 3.16: 26622 3.16 - 3.74: 47949 3.74 - 4.32: 73418 4.32 - 4.90: 122446 Nonbonded interactions: 270715 Sorted by model distance: nonbonded pdb=" O VAL G1577 " pdb=" OG SER G1580 " model vdw 2.007 3.040 nonbonded pdb=" OE2 GLU N 107 " pdb=" OG1 THR N 134 " model vdw 2.042 3.040 nonbonded pdb=" O LEU C 81 " pdb=" OH TYR C 86 " model vdw 2.098 3.040 nonbonded pdb=" O LEU F 81 " pdb=" OH TYR F 86 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASN J1568 " pdb=" OD1 ASN L1567 " model vdw 2.142 3.040 ... (remaining 270710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'H' and (resid 1557 through 1589 or (resid 1590 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'I' and (resid 1557 through 1589 or (resid 1590 and (name N or name CA or \ name C or name O or name CB )))) selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 7.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.170 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 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 : 0.002 0.042 32741 Z= 0.111 Angle : 0.464 10.496 44626 Z= 0.252 Chirality : 0.042 0.143 5157 Planarity : 0.002 0.050 5759 Dihedral : 13.364 88.575 11577 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.03 % Allowed : 0.06 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 4092 helix: 0.56 (0.22), residues: 609 sheet: 0.33 (0.13), residues: 1524 loop : -0.27 (0.15), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 150 TYR 0.025 0.001 TYR M 87 PHE 0.009 0.001 PHE O 346 TRP 0.063 0.001 TRP N 89 HIS 0.008 0.001 HIS M 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (32741) covalent geometry : angle 0.46426 / 0.25 (44626) hydrogen bonds : bond 0.15917 / 11.02 ( 901) hydrogen bonds : angle 7.09926 / 4.97 ( 2409) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 1.226 Fit side-chains REVERT: Y 3 THR cc_start: 0.8560 (p) cc_final: 0.8288 (p) REVERT: Y 73 ASP cc_start: 0.8606 (t0) cc_final: 0.8363 (t70) REVERT: a 153 ASP cc_start: 0.8071 (p0) cc_final: 0.7863 (p0) REVERT: b 71 LYS cc_start: 0.6787 (tppt) cc_final: 0.6517 (tptp) REVERT: b 177 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8563 (mm-30) REVERT: c 23 ASP cc_start: 0.7274 (t0) cc_final: 0.6766 (t0) REVERT: M 77 SER cc_start: 0.8547 (t) cc_final: 0.8342 (t) REVERT: M 129 SER cc_start: 0.8740 (t) cc_final: 0.8348 (p) REVERT: O 27 LEU cc_start: 0.8577 (mp) cc_final: 0.8171 (tt) REVERT: O 29 MET cc_start: 0.9270 (mmm) cc_final: 0.8882 (mmm) REVERT: O 140 ILE cc_start: 0.8506 (mm) cc_final: 0.8298 (mm) REVERT: O 147 GLU cc_start: 0.8351 (tt0) cc_final: 0.8062 (tt0) REVERT: O 234 SER cc_start: 0.8090 (t) cc_final: 0.7765 (p) REVERT: D 79 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7631 (mt-10) REVERT: E 32 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8502 (mtmt) REVERT: F 32 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8086 (mttt) REVERT: Z 121 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8367 (mt-10) outliers start: 1 outliers final: 1 residues processed: 460 average time/residue: 0.6493 time to fit residues: 358.0295 Evaluate side-chains 333 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 122 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 31 ASN b 94 GLN d 124 GLN A 627 ASN M 116 GLN M 312 HIS N 199 ASN N 312 HIS O 199 ASN O 312 HIS B 575 ASN B 593 GLN B 621 GLN B 649 GLN C 567 ASN C 621 GLN E 627 ASN F 55 ASN I1569 GLN K1566 GLN K1567 ASN L1567 ASN Z 31 ASN Z 94 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.084281 restraints weight = 44380.775| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.99 r_work: 0.2849 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32741 Z= 0.126 Angle : 0.493 9.760 44626 Z= 0.260 Chirality : 0.043 0.169 5157 Planarity : 0.003 0.032 5759 Dihedral : 4.553 87.119 4451 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.52 % Allowed : 6.49 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 4092 helix: 0.72 (0.22), residues: 605 sheet: 0.32 (0.13), residues: 1551 loop : -0.29 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 350 TYR 0.022 0.001 TYR M 87 PHE 0.013 0.001 PHE Y 139 TRP 0.031 0.001 TRP M 89 HIS 0.008 0.001 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (32741) covalent geometry : angle 0.49343 / 0.26 (44626) hydrogen bonds : bond 0.03255 / 2.23 ( 901) hydrogen bonds : angle 5.30422 / 3.76 ( 2409) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 3 THR cc_start: 0.8589 (p) cc_final: 0.8319 (p) REVERT: b 37 ASP cc_start: 0.8255 (t70) cc_final: 0.7798 (m-30) REVERT: b 71 LYS cc_start: 0.6781 (tppt) cc_final: 0.6247 (tptp) REVERT: b 177 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8516 (mm-30) REVERT: c 23 ASP cc_start: 0.7469 (t0) cc_final: 0.6800 (t0) REVERT: d 117 ASP cc_start: 0.8745 (m-30) cc_final: 0.8260 (m-30) REVERT: M 129 SER cc_start: 0.8740 (t) cc_final: 0.8171 (p) REVERT: N 147 GLU cc_start: 0.8226 (tt0) cc_final: 0.7864 (mt-10) REVERT: O 27 LEU cc_start: 0.8634 (mp) cc_final: 0.8288 (tt) REVERT: O 147 GLU cc_start: 0.8552 (tt0) cc_final: 0.8223 (tt0) REVERT: O 234 SER cc_start: 0.8286 (t) cc_final: 0.7960 (p) REVERT: B 58 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: C 617 ILE cc_start: 0.8581 (pt) cc_final: 0.8210 (mm) REVERT: D 79 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7847 (mt-10) REVERT: E 649 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8554 (pt0) REVERT: F 48 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8536 (tt0) REVERT: Z 19 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8250 (mttm) REVERT: Z 177 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8745 (mm-30) outliers start: 54 outliers final: 15 residues processed: 368 average time/residue: 0.6281 time to fit residues: 276.8716 Evaluate side-chains 326 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 307 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 285 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain E residue 601 GLU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 649 GLN Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 611 ASP Chi-restraints excluded: chain K residue 1566 GLN Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 25 optimal weight: 4.9990 chunk 277 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 392 optimal weight: 5.9990 chunk 176 optimal weight: 0.0870 chunk 152 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 315 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 31 ASN A 58 GLN M 116 GLN O 264 HIS B 123 ASN C 621 GLN J1613 ASN K1613 ASN Z 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.080272 restraints weight = 44877.767| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.98 r_work: 0.2772 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32741 Z= 0.182 Angle : 0.522 7.825 44626 Z= 0.275 Chirality : 0.044 0.173 5157 Planarity : 0.003 0.026 5759 Dihedral : 4.826 87.600 4449 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.72 % Allowed : 8.47 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4092 helix: 0.59 (0.22), residues: 605 sheet: 0.21 (0.13), residues: 1551 loop : -0.37 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 606 TYR 0.013 0.001 TYR C 604 PHE 0.016 0.001 PHE Y 139 TRP 0.043 0.001 TRP M 89 HIS 0.010 0.001 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (32741) covalent geometry : angle 0.52248 / 0.28 (44626) hydrogen bonds : bond 0.03308 / 2.27 ( 901) hydrogen bonds : angle 5.24539 / 3.71 ( 2409) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 317 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: Y 153 ASP cc_start: 0.8446 (p0) cc_final: 0.8216 (p0) REVERT: a 79 ASP cc_start: 0.9108 (t0) cc_final: 0.8794 (m-30) REVERT: b 37 ASP cc_start: 0.8368 (t70) cc_final: 0.8017 (t70) REVERT: b 71 LYS cc_start: 0.6825 (tppt) cc_final: 0.6373 (tptp) REVERT: c 23 ASP cc_start: 0.7530 (t0) cc_final: 0.6917 (t0) REVERT: d 37 ASP cc_start: 0.8456 (t0) cc_final: 0.8090 (t0) REVERT: d 117 ASP cc_start: 0.8742 (m-30) cc_final: 0.8266 (m-30) REVERT: A 141 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: N 144 ASP cc_start: 0.7851 (p0) cc_final: 0.7649 (p0) REVERT: N 342 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8505 (tpp) REVERT: O 27 LEU cc_start: 0.8654 (mp) cc_final: 0.8360 (tt) REVERT: O 147 GLU cc_start: 0.8599 (tt0) cc_final: 0.8211 (tt0) REVERT: O 234 SER cc_start: 0.8309 (t) cc_final: 0.7995 (p) REVERT: B 58 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: C 617 ILE cc_start: 0.8563 (pt) cc_final: 0.8363 (mm) REVERT: D 79 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7984 (mt-10) REVERT: E 649 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8588 (pt0) REVERT: F 48 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: F 141 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: Z 19 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8187 (mttm) REVERT: Z 89 MET cc_start: 0.8830 (mmp) cc_final: 0.8578 (mmp) REVERT: Z 148 ASP cc_start: 0.7980 (m-30) cc_final: 0.7186 (p0) outliers start: 61 outliers final: 26 residues processed: 352 average time/residue: 0.6060 time to fit residues: 257.0765 Evaluate side-chains 326 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 158 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 175 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 116 GLN Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 342 MET Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain E residue 601 GLU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 649 GLN Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 611 ASP Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 175 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 379 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 349 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 383 optimal weight: 7.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 31 ASN M 90 ASN M 116 GLN M 312 HIS B 123 ASN E 567 ASN G1613 ASN K1613 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.081384 restraints weight = 44579.416| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.98 r_work: 0.2803 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32741 Z= 0.127 Angle : 0.469 7.405 44626 Z= 0.249 Chirality : 0.042 0.155 5157 Planarity : 0.003 0.027 5759 Dihedral : 4.636 84.491 4449 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.81 % Allowed : 9.46 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 4092 helix: 0.73 (0.22), residues: 607 sheet: 0.23 (0.13), residues: 1515 loop : -0.37 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 167 TYR 0.011 0.001 TYR C 620 PHE 0.010 0.001 PHE Y 139 TRP 0.020 0.001 TRP M 89 HIS 0.011 0.001 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (32741) covalent geometry : angle 0.46933 / 0.25 (44626) hydrogen bonds : bond 0.02777 / 1.89 ( 901) hydrogen bonds : angle 5.03078 / 3.55 ( 2409) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 313 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: Y 153 ASP cc_start: 0.8380 (p0) cc_final: 0.8122 (p0) REVERT: b 37 ASP cc_start: 0.8341 (t70) cc_final: 0.7990 (t70) REVERT: b 71 LYS cc_start: 0.6789 (tppt) cc_final: 0.6326 (tptp) REVERT: c 23 ASP cc_start: 0.7567 (t0) cc_final: 0.7068 (t0) REVERT: c 121 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: d 117 ASP cc_start: 0.8747 (m-30) cc_final: 0.8308 (m-30) REVERT: A 141 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: N 233 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8117 (mt-10) REVERT: N 299 MET cc_start: 0.9347 (ptp) cc_final: 0.9137 (ptt) REVERT: O 27 LEU cc_start: 0.8610 (mp) cc_final: 0.8317 (tt) REVERT: O 147 GLU cc_start: 0.8552 (tt0) cc_final: 0.8202 (tt0) REVERT: O 234 SER cc_start: 0.8346 (t) cc_final: 0.8020 (p) REVERT: E 48 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: E 649 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8550 (pt0) REVERT: F 141 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: Z 148 ASP cc_start: 0.7885 (m-30) cc_final: 0.7099 (p0) outliers start: 64 outliers final: 31 residues processed: 352 average time/residue: 0.5887 time to fit residues: 250.2229 Evaluate side-chains 325 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 175 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 342 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 601 GLU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 649 GLN Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 611 ASP Chi-restraints excluded: chain G residue 1607 MET Chi-restraints excluded: chain Z residue 172 LEU Chi-restraints excluded: chain Z residue 175 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 171 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 243 optimal weight: 0.0770 chunk 256 optimal weight: 5.9990 chunk 397 optimal weight: 0.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 31 ASN A 58 GLN M 116 GLN B 123 ASN B 592 GLN D 575 ASN E 58 GLN E 567 ASN F 567 ASN G1613 ASN J1613 ASN K1613 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.079912 restraints weight = 44842.283| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.97 r_work: 0.2787 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32741 Z= 0.154 Angle : 0.490 8.046 44626 Z= 0.259 Chirality : 0.043 0.163 5157 Planarity : 0.003 0.027 5759 Dihedral : 4.734 83.876 4449 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.29 % Allowed : 9.66 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4092 helix: 0.71 (0.22), residues: 608 sheet: 0.16 (0.13), residues: 1545 loop : -0.35 (0.15), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 8 TYR 0.014 0.001 TYR C 620 PHE 0.012 0.001 PHE Y 139 TRP 0.018 0.001 TRP M 89 HIS 0.011 0.001 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (32741) covalent geometry : angle 0.49029 / 0.26 (44626) hydrogen bonds : bond 0.02897 / 1.97 ( 901) hydrogen bonds : angle 5.06731 / 3.59 ( 2409) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: Y 153 ASP cc_start: 0.8544 (p0) cc_final: 0.8249 (p0) REVERT: Y 193 TYR cc_start: 0.8937 (t80) cc_final: 0.8734 (t80) REVERT: a 44 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8856 (mtpt) REVERT: b 37 ASP cc_start: 0.8379 (t70) cc_final: 0.7985 (t70) REVERT: b 71 LYS cc_start: 0.6696 (tppt) cc_final: 0.6227 (tptp) REVERT: b 177 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8590 (mm-30) REVERT: c 23 ASP cc_start: 0.7592 (t0) cc_final: 0.7027 (t0) REVERT: d 37 ASP cc_start: 0.8452 (t0) cc_final: 0.8114 (t70) REVERT: d 117 ASP cc_start: 0.8761 (m-30) cc_final: 0.8312 (m-30) REVERT: A 1 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8060 (tpt) REVERT: A 141 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: N 144 ASP cc_start: 0.7914 (p0) cc_final: 0.7712 (p0) REVERT: N 147 GLU cc_start: 0.8196 (tt0) cc_final: 0.7847 (mt-10) REVERT: N 175 MET cc_start: 0.8652 (mmm) cc_final: 0.8102 (tpp) REVERT: N 233 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8154 (mt-10) REVERT: N 299 MET cc_start: 0.9319 (ptp) cc_final: 0.9112 (ptt) REVERT: O 27 LEU cc_start: 0.8627 (mp) cc_final: 0.8300 (tt) REVERT: O 107 GLU cc_start: 0.9084 (mp0) cc_final: 0.8852 (mp0) REVERT: O 147 GLU cc_start: 0.8544 (tt0) cc_final: 0.8206 (tt0) REVERT: O 234 SER cc_start: 0.8387 (t) cc_final: 0.8073 (p) REVERT: D 79 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7915 (mt-10) REVERT: E 48 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: E 649 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8534 (pt0) REVERT: F 141 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: Z 19 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8125 (mttm) REVERT: Z 148 ASP cc_start: 0.7962 (m-30) cc_final: 0.7147 (p0) outliers start: 81 outliers final: 42 residues processed: 356 average time/residue: 0.6365 time to fit residues: 273.0828 Evaluate side-chains 336 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 175 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 342 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 601 GLU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 649 GLN Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 611 ASP Chi-restraints excluded: chain F residue 649 GLN Chi-restraints excluded: chain K residue 1607 MET Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 175 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 322 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 260 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 400 optimal weight: 0.3980 chunk 380 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 31 ASN a 124 GLN M 116 GLN N 199 ASN B 123 ASN D 575 ASN E 58 GLN E 567 ASN F 567 ASN F 591 ASN G1568 ASN G1613 ASN J1613 ASN K1613 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.080332 restraints weight = 44664.867| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.96 r_work: 0.2782 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 32741 Z= 0.154 Angle : 0.486 7.278 44626 Z= 0.258 Chirality : 0.043 0.162 5157 Planarity : 0.003 0.027 5759 Dihedral : 4.734 85.985 4449 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.26 % Allowed : 9.99 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4092 helix: 0.74 (0.22), residues: 608 sheet: 0.13 (0.13), residues: 1545 loop : -0.35 (0.15), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.014 0.001 TYR C 620 PHE 0.011 0.001 PHE Y 139 TRP 0.014 0.001 TRP M 89 HIS 0.011 0.001 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (32741) covalent geometry : angle 0.48644 / 0.26 (44626) hydrogen bonds : bond 0.02856 / 1.94 ( 901) hydrogen bonds : angle 5.03674 / 3.56 ( 2409) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 306 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: a 44 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8884 (mtpt) REVERT: b 37 ASP cc_start: 0.8369 (t70) cc_final: 0.7989 (t70) REVERT: b 71 LYS cc_start: 0.6726 (tppt) cc_final: 0.6268 (tptp) REVERT: b 177 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8588 (mm-30) REVERT: c 23 ASP cc_start: 0.7642 (t0) cc_final: 0.7114 (t0) REVERT: d 37 ASP cc_start: 0.8444 (t0) cc_final: 0.8105 (t70) REVERT: d 117 ASP cc_start: 0.8754 (m-30) cc_final: 0.8290 (m-30) REVERT: A 1 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8233 (tpt) REVERT: A 141 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: M 329 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7646 (p) REVERT: N 175 MET cc_start: 0.8738 (mmm) cc_final: 0.8200 (tpp) REVERT: N 233 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8226 (mt-10) REVERT: N 299 MET cc_start: 0.9337 (ptp) cc_final: 0.9128 (ptt) REVERT: O 27 LEU cc_start: 0.8636 (mp) cc_final: 0.8315 (tt) REVERT: O 107 GLU cc_start: 0.9129 (mp0) cc_final: 0.8907 (mp0) REVERT: O 147 GLU cc_start: 0.8564 (tt0) cc_final: 0.8240 (tt0) REVERT: O 234 SER cc_start: 0.8451 (t) cc_final: 0.8139 (p) REVERT: D 79 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7960 (mt-10) REVERT: E 69 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8140 (m-70) REVERT: E 649 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8563 (pt0) REVERT: F 141 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: Z 19 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8140 (mttm) REVERT: Z 148 ASP cc_start: 0.7955 (m-30) cc_final: 0.7173 (p0) outliers start: 80 outliers final: 49 residues processed: 356 average time/residue: 0.6272 time to fit residues: 269.1380 Evaluate side-chains 340 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 284 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 158 SER Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 62 ASN Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 62 ASN Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 175 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 342 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 601 GLU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 649 GLN Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 611 ASP Chi-restraints excluded: chain F residue 649 GLN Chi-restraints excluded: chain G residue 1607 MET Chi-restraints excluded: chain K residue 1607 MET Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 71 LYS Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 175 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 379 optimal weight: 5.9990 chunk 307 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 326 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 368 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 31 ASN A 58 GLN M 116 GLN N 199 ASN O 231 ASN B 123 ASN D 575 ASN E 58 GLN E 567 ASN F 567 ASN F 591 ASN G1613 ASN J1613 ASN K1613 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.080604 restraints weight = 44447.889| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.94 r_work: 0.2777 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32741 Z= 0.156 Angle : 0.491 7.541 44626 Z= 0.260 Chirality : 0.043 0.161 5157 Planarity : 0.003 0.027 5759 Dihedral : 4.740 87.249 4449 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.29 % Allowed : 10.42 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4092 helix: 0.75 (0.22), residues: 608 sheet: 0.09 (0.13), residues: 1545 loop : -0.34 (0.15), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 8 TYR 0.016 0.001 TYR C 620 PHE 0.011 0.001 PHE Y 139 TRP 0.011 0.001 TRP M 89 HIS 0.009 0.001 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (32741) covalent geometry : angle 0.49079 / 0.26 (44626) hydrogen bonds : bond 0.02863 / 1.95 ( 901) hydrogen bonds : angle 5.04622 / 3.56 ( 2409) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 292 time to evaluate : 1.274 Fit side-chains REVERT: a 44 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8885 (mtpt) REVERT: a 154 ASN cc_start: 0.8566 (p0) cc_final: 0.8286 (p0) REVERT: b 37 ASP cc_start: 0.8369 (t70) cc_final: 0.7960 (t70) REVERT: b 71 LYS cc_start: 0.6723 (tppt) cc_final: 0.6262 (tptp) REVERT: c 23 ASP cc_start: 0.7691 (t0) cc_final: 0.7247 (t0) REVERT: d 37 ASP cc_start: 0.8442 (t0) cc_final: 0.8099 (t70) REVERT: d 117 ASP cc_start: 0.8759 (m-30) cc_final: 0.8293 (m-30) REVERT: A 1 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8241 (tpt) REVERT: A 141 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: M 329 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7672 (p) REVERT: N 147 GLU cc_start: 0.8214 (tt0) cc_final: 0.7799 (mt-10) REVERT: N 175 MET cc_start: 0.8774 (mmm) cc_final: 0.8240 (tpp) REVERT: N 233 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8237 (mt-10) REVERT: N 299 MET cc_start: 0.9336 (ptp) cc_final: 0.9114 (ptt) REVERT: O 27 LEU cc_start: 0.8641 (mp) cc_final: 0.8315 (tt) REVERT: O 107 GLU cc_start: 0.9128 (mp0) cc_final: 0.8873 (mp0) REVERT: O 147 GLU cc_start: 0.8538 (tt0) cc_final: 0.8189 (tt0) REVERT: O 234 SER cc_start: 0.8458 (t) cc_final: 0.8132 (p) REVERT: D 79 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7946 (mt-10) REVERT: E 69 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.8141 (m-70) REVERT: E 649 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8550 (pt0) REVERT: F 43 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8268 (mp) REVERT: F 141 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: Z 19 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8072 (mttm) REVERT: Z 148 ASP cc_start: 0.7960 (m-30) cc_final: 0.7172 (p0) outliers start: 81 outliers final: 50 residues processed: 343 average time/residue: 0.6598 time to fit residues: 272.0374 Evaluate side-chains 343 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 285 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 158 SER Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 62 ASN Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 62 ASN Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 175 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 342 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 601 GLU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 649 GLN Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 611 ASP Chi-restraints excluded: chain F residue 649 GLN Chi-restraints excluded: chain G residue 1607 MET Chi-restraints excluded: chain K residue 1607 MET Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 175 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 244 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 384 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 116 GLN B 123 ASN D 575 ASN E 58 GLN E 567 ASN F 58 GLN F 567 ASN G1613 ASN I1569 GLN J1613 ASN K1613 ASN Z 31 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.102809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.077743 restraints weight = 45238.061| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.96 r_work: 0.2717 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 32741 Z= 0.246 Angle : 0.560 8.677 44626 Z= 0.294 Chirality : 0.045 0.182 5157 Planarity : 0.003 0.027 5759 Dihedral : 5.097 88.230 4449 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.37 % Allowed : 10.70 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4092 helix: 0.47 (0.21), residues: 611 sheet: 0.03 (0.13), residues: 1533 loop : -0.45 (0.15), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 167 TYR 0.023 0.002 TYR C 142 PHE 0.014 0.002 PHE b 139 TRP 0.013 0.001 TRP M 89 HIS 0.014 0.002 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (32741) covalent geometry : angle 0.56035 / 0.29 (44626) hydrogen bonds : bond 0.03344 / 2.26 ( 901) hydrogen bonds : angle 5.29596 / 3.74 ( 2409) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 284 time to evaluate : 1.306 Fit side-chains REVERT: a 44 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8879 (mtpt) REVERT: b 44 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8978 (mtpt) REVERT: b 71 LYS cc_start: 0.6694 (tppt) cc_final: 0.6210 (tptp) REVERT: b 177 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8564 (mm-30) REVERT: c 23 ASP cc_start: 0.7684 (t0) cc_final: 0.7193 (t0) REVERT: d 117 ASP cc_start: 0.8811 (m-30) cc_final: 0.8337 (m-30) REVERT: A 141 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: M 329 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7833 (p) REVERT: N 233 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8337 (mt-10) REVERT: O 27 LEU cc_start: 0.8673 (mp) cc_final: 0.8316 (tt) REVERT: O 107 GLU cc_start: 0.9149 (mp0) cc_final: 0.8910 (mp0) REVERT: D 79 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7978 (mt-10) REVERT: E 69 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.8112 (m-70) REVERT: E 649 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8563 (pt0) REVERT: F 8 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8207 (mtm180) REVERT: F 43 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8238 (mp) REVERT: F 141 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: Z 148 ASP cc_start: 0.7934 (m-30) cc_final: 0.7141 (p0) outliers start: 84 outliers final: 56 residues processed: 338 average time/residue: 0.6720 time to fit residues: 272.4065 Evaluate side-chains 337 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 274 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 158 SER Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 62 ASN Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 62 ASN Chi-restraints excluded: chain d residue 175 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 342 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 601 GLU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 649 GLN Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 579 ILE Chi-restraints excluded: chain F residue 611 ASP Chi-restraints excluded: chain F residue 649 GLN Chi-restraints excluded: chain G residue 1606 SER Chi-restraints excluded: chain G residue 1607 MET Chi-restraints excluded: chain K residue 1607 MET Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 175 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 369 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 367 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 124 GLN M 116 GLN B 123 ASN E 58 GLN E 567 ASN F 567 ASN G1613 ASN K1613 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.082200 restraints weight = 44161.156| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.94 r_work: 0.2815 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32741 Z= 0.098 Angle : 0.456 7.421 44626 Z= 0.242 Chirality : 0.042 0.146 5157 Planarity : 0.003 0.027 5759 Dihedral : 4.599 87.686 4449 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.75 % Allowed : 11.63 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 4092 helix: 0.82 (0.22), residues: 611 sheet: 0.06 (0.13), residues: 1545 loop : -0.33 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 213 TYR 0.014 0.001 TYR D 620 PHE 0.009 0.001 PHE O 297 TRP 0.009 0.001 TRP a 173 HIS 0.012 0.001 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (32741) covalent geometry : angle 0.45584 / 0.24 (44626) hydrogen bonds : bond 0.02499 / 1.70 ( 901) hydrogen bonds : angle 4.95522 / 3.51 ( 2409) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 303 time to evaluate : 1.327 Fit side-chains REVERT: b 71 LYS cc_start: 0.6692 (tppt) cc_final: 0.6245 (tptp) REVERT: b 177 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8520 (mm-30) REVERT: c 23 ASP cc_start: 0.7753 (t0) cc_final: 0.7321 (t0) REVERT: d 117 ASP cc_start: 0.8760 (m-30) cc_final: 0.8243 (m-30) REVERT: A 48 GLN cc_start: 0.8817 (tt0) cc_final: 0.8595 (tt0) REVERT: A 141 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: M 329 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7563 (p) REVERT: N 147 GLU cc_start: 0.8218 (tt0) cc_final: 0.7796 (mt-10) REVERT: N 233 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8218 (mt-10) REVERT: N 299 MET cc_start: 0.9347 (ptp) cc_final: 0.9117 (ptm) REVERT: O 27 LEU cc_start: 0.8528 (mp) cc_final: 0.8239 (tt) REVERT: O 107 GLU cc_start: 0.9102 (mp0) cc_final: 0.8897 (mp0) REVERT: O 234 SER cc_start: 0.8531 (t) cc_final: 0.8239 (p) REVERT: D 79 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7963 (mt-10) REVERT: E 649 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8550 (pt0) REVERT: Z 1 MET cc_start: 0.4752 (OUTLIER) cc_final: 0.4356 (tmt) outliers start: 62 outliers final: 38 residues processed: 345 average time/residue: 0.6463 time to fit residues: 268.4750 Evaluate side-chains 330 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 62 ASN Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 175 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 342 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 601 GLU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 649 GLN Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 611 ASP Chi-restraints excluded: chain G residue 1606 SER Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 71 LYS Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 327 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 280 optimal weight: 0.6980 chunk 342 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 243 optimal weight: 0.0030 chunk 149 optimal weight: 9.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 124 GLN A 58 GLN M 116 GLN B 123 ASN D 621 GLN E 58 GLN E 567 ASN F 567 ASN G1613 ASN J1613 ASN K1613 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.080611 restraints weight = 44496.070| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.94 r_work: 0.2786 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32741 Z= 0.151 Angle : 0.494 7.978 44626 Z= 0.260 Chirality : 0.043 0.159 5157 Planarity : 0.003 0.027 5759 Dihedral : 4.693 89.449 4449 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.61 % Allowed : 11.91 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4092 helix: 0.77 (0.22), residues: 611 sheet: 0.05 (0.13), residues: 1545 loop : -0.35 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 8 TYR 0.013 0.001 TYR C 620 PHE 0.011 0.001 PHE b 139 TRP 0.010 0.001 TRP F 570 HIS 0.013 0.001 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (32741) covalent geometry : angle 0.49358 / 0.26 (44626) hydrogen bonds : bond 0.02809 / 1.91 ( 901) hydrogen bonds : angle 5.00792 / 3.54 ( 2409) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 1.197 Fit side-chains REVERT: b 71 LYS cc_start: 0.6721 (tppt) cc_final: 0.6268 (tptp) REVERT: b 177 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8518 (mm-30) REVERT: c 23 ASP cc_start: 0.7741 (t0) cc_final: 0.7314 (t0) REVERT: d 117 ASP cc_start: 0.8782 (m-30) cc_final: 0.8283 (m-30) REVERT: A 141 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: M 170 ASP cc_start: 0.8324 (p0) cc_final: 0.8007 (p0) REVERT: M 329 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7657 (p) REVERT: N 147 GLU cc_start: 0.8196 (tt0) cc_final: 0.7787 (mt-10) REVERT: N 233 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8271 (mt-10) REVERT: N 299 MET cc_start: 0.9336 (ptp) cc_final: 0.9110 (ptm) REVERT: O 27 LEU cc_start: 0.8640 (mp) cc_final: 0.8291 (tt) REVERT: O 29 MET cc_start: 0.9344 (mmm) cc_final: 0.9094 (mmm) REVERT: O 107 GLU cc_start: 0.9128 (mp0) cc_final: 0.8898 (mp0) REVERT: O 234 SER cc_start: 0.8537 (t) cc_final: 0.8228 (p) REVERT: D 79 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7948 (mt-10) REVERT: E 48 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: E 649 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8552 (pt0) REVERT: J 1589 ASN cc_start: 0.6292 (OUTLIER) cc_final: 0.5915 (m-40) REVERT: Z 1 MET cc_start: 0.4811 (OUTLIER) cc_final: 0.4492 (tmt) REVERT: Z 148 ASP cc_start: 0.7904 (m-30) cc_final: 0.7134 (p0) outliers start: 57 outliers final: 40 residues processed: 320 average time/residue: 0.6566 time to fit residues: 252.7432 Evaluate side-chains 326 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 280 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 62 ASN Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 175 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 342 MET Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 601 GLU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 649 GLN Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 611 ASP Chi-restraints excluded: chain J residue 1589 ASN Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 62 ASN Chi-restraints excluded: chain Z residue 71 LYS Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 317 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 336 optimal weight: 0.0570 chunk 53 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 123 optimal weight: 0.0040 overall best weight: 1.6114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 31 ASN a 124 GLN A 58 GLN M 116 GLN B 123 ASN E 58 GLN E 567 ASN F 567 ASN G1613 ASN J1613 ASN K1613 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.080845 restraints weight = 44452.849| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.94 r_work: 0.2791 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32741 Z= 0.141 Angle : 0.485 7.781 44626 Z= 0.256 Chirality : 0.042 0.156 5157 Planarity : 0.003 0.027 5759 Dihedral : 4.656 89.982 4449 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.72 % Allowed : 11.77 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4092 helix: 0.78 (0.22), residues: 613 sheet: 0.07 (0.13), residues: 1545 loop : -0.36 (0.15), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 167 TYR 0.014 0.001 TYR D 620 PHE 0.011 0.001 PHE b 139 TRP 0.009 0.001 TRP F 570 HIS 0.013 0.001 HIS N 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (32741) covalent geometry : angle 0.48467 / 0.26 (44626) hydrogen bonds : bond 0.02746 / 1.87 ( 901) hydrogen bonds : angle 4.98597 / 3.52 ( 2409) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11250.36 seconds wall clock time: 192 minutes 29.64 seconds (11549.64 seconds total)