Starting phenix.real_space_refine on Thu Feb 15 01:28:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drc_30826/02_2024/7drc_30826.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drc_30826/02_2024/7drc_30826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drc_30826/02_2024/7drc_30826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drc_30826/02_2024/7drc_30826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drc_30826/02_2024/7drc_30826.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drc_30826/02_2024/7drc_30826.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6797 2.51 5 N 1727 2.21 5 O 2171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10737 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain: "C" Number of atoms: 7114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7114 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 39, 'TRANS': 866} Chain: "B" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1360 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 13, 'TRANS': 162} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.99, per 1000 atoms: 0.56 Number of scatterers: 10737 At special positions: 0 Unit cell: (127.32, 98.673, 128.381, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2171 8.00 N 1727 7.00 C 6797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 644 " distance=2.02 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 67 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN F 5 " - " MAN F 6 " ALPHA1-3 " BMA F 3 " - " MAN F 8 " " MAN F 4 " - " MAN F 7 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG B1000 " - " ASN B 82 " " NAG B1001 " - " ASN B 106 " " NAG B1002 " - " ASN B 117 " " NAG B1003 " - " ASN B 152 " " NAG C1001 " - " ASN C 159 " " NAG C1002 " - " ASN C 234 " " NAG C1003 " - " ASN C 261 " " NAG C1004 " - " ASN C 532 " " NAG C1005 " - " ASN C 542 " " NAG C1006 " - " ASN C 591 " " NAG C1007 " - " ASN C 660 " " NAG C1008 " - " ASN C 855 " " NAG C1009 " - " ASN C 888 " " NAG D 1 " - " ASN B 186 " " NAG E 1 " - " ASN C 73 " " NAG F 1 " - " ASN C 143 " " NAG G 1 " - " ASN C 311 " " NAG H 1 " - " ASN C 481 " " NAG I 1 " - " ASN C 562 " " NAG J 1 " - " ASN C 647 " " NAG K 1 " - " ASN C 767 " " NAG L 1 " - " ASN C 848 " Time building additional restraints: 4.88 Conformation dependent library (CDL) restraints added in 1.7 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 17 sheets defined 18.5% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.565A pdb=" N GLY C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 45 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 105 through 111 removed outlier: 3.824A pdb=" N LEU C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.787A pdb=" N ILE C 133 " --> pdb=" O PRO C 130 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C 136 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.607A pdb=" N PHE C 157 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 158 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 337 through 340 removed outlier: 3.954A pdb=" N ARG C 340 " --> pdb=" O SER C 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 340' Processing helix chain 'C' and resid 360 through 363 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 428 through 434 removed outlier: 3.836A pdb=" N GLY C 432 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 434 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 457 removed outlier: 3.697A pdb=" N MET C 454 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 455 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 456 " --> pdb=" O SER C 453 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 457 " --> pdb=" O MET C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 457' Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.722A pdb=" N CYS C 621 " --> pdb=" O SER C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 672 Processing helix chain 'C' and resid 714 through 719 removed outlier: 3.773A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 745 removed outlier: 3.641A pdb=" N LEU C 744 " --> pdb=" O ILE C 741 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 745 " --> pdb=" O CYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 768 removed outlier: 3.526A pdb=" N PHE C 768 " --> pdb=" O PHE C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 839 removed outlier: 3.670A pdb=" N MET C 838 " --> pdb=" O PRO C 835 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 839 " --> pdb=" O LYS C 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 835 through 839' Processing helix chain 'C' and resid 861 through 865 Processing helix chain 'C' and resid 883 through 889 removed outlier: 3.514A pdb=" N LEU C 889 " --> pdb=" O LEU C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 915 removed outlier: 3.509A pdb=" N PHE C 915 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 920 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.519A pdb=" N ASN B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 removed outlier: 4.123A pdb=" N GLY B 92 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 93 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 94 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.700A pdb=" N LEU B 115 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.607A pdb=" N THR B 164 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.646A pdb=" N PHE B 189 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B 191 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 192 " --> pdb=" O PHE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.574A pdb=" N VAL A 36 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 59 removed outlier: 4.782A pdb=" N SER A 48 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 72 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA A 64 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 58 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 63 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A 235 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 65 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP A 71 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR A 227 " --> pdb=" O TRP A 71 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS A 105 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 236 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS A 103 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA A 238 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 3.674A pdb=" N ALA A 158 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA A 142 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 119 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ALA A 143 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A 117 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP A 118 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR A 221 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 120 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 219 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP A 122 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 217 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 124 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 149 Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.679A pdb=" N GLU C 71 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 80 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP C 118 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 82 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU C 117 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU C 190 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 215 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU C 318 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 393 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 416 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU C 440 " --> pdb=" O ASP C 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.367A pdb=" N GLY C 151 " --> pdb=" O ILE C 174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.548A pdb=" N LEU C 357 " --> pdb=" O MET C 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 424 through 426 removed outlier: 7.070A pdb=" N GLY C 425 " --> pdb=" O GLU C 448 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 471 through 474 removed outlier: 4.483A pdb=" N GLY C 472 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 487 through 489 removed outlier: 6.331A pdb=" N LEU C 488 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 512 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE C 585 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU C 630 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 654 " --> pdb=" O TYR C 679 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 678 " --> pdb=" O ASP C 702 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C 701 " --> pdb=" O SER C 727 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C 726 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU C 750 " --> pdb=" O ASP C 824 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE C 823 " --> pdb=" O ASN C 848 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 847 " --> pdb=" O ASP C 872 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 569 through 570 removed outlier: 5.582A pdb=" N GLY C 570 " --> pdb=" O SER C 593 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE C 592 " --> pdb=" O GLN C 612 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE C 614 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY C 594 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE C 613 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 638 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY C 615 " --> pdb=" O SER C 638 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLU C 640 " --> pdb=" O GLY C 615 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE C 637 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 662 " --> pdb=" O PHE C 637 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY C 639 " --> pdb=" O SER C 662 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE C 661 " --> pdb=" O SER C 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 782 through 789 removed outlier: 3.931A pdb=" N GLY C 787 " --> pdb=" O TYR C 792 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR C 792 " --> pdb=" O GLY C 787 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 802 through 806 Processing sheet with id=AB5, first strand: chain 'C' and resid 831 through 832 removed outlier: 5.508A pdb=" N GLY C 832 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU C 854 " --> pdb=" O GLN C 877 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 903 through 904 removed outlier: 4.174A pdb=" N GLY C 904 " --> pdb=" O GLN C 925 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.618A pdb=" N ARG B 75 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 76 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP B 125 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 148 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 185 hydrogen bonds defined for protein. 360 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: 3.85 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3355 1.35 - 1.47: 2742 1.47 - 1.59: 4791 1.59 - 1.72: 0 1.72 - 1.84: 62 Bond restraints: 10950 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.20e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C1 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" C1 NAG C1006 " pdb=" O5 NAG C1006 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 ... (remaining 10945 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.74: 318 106.74 - 113.56: 6323 113.56 - 120.38: 3726 120.38 - 127.20: 4396 127.20 - 134.02: 103 Bond angle restraints: 14866 Sorted by residual: angle pdb=" C3 MAN F 5 " pdb=" C2 MAN F 5 " pdb=" O2 MAN F 5 " ideal model delta sigma weight residual 111.77 104.34 7.43 3.00e+00 1.11e-01 6.14e+00 angle pdb=" CA LEU C 931 " pdb=" CB LEU C 931 " pdb=" CG LEU C 931 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.04e+00 angle pdb=" CA GLU C 123 " pdb=" CB GLU C 123 " pdb=" CG GLU C 123 " ideal model delta sigma weight residual 114.10 118.95 -4.85 2.00e+00 2.50e-01 5.88e+00 angle pdb=" CA MET A 138 " pdb=" CB MET A 138 " pdb=" CG MET A 138 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.38e+00 angle pdb=" C ILE A 137 " pdb=" N MET A 138 " pdb=" CA MET A 138 " ideal model delta sigma weight residual 121.42 124.73 -3.31 1.43e+00 4.89e-01 5.37e+00 ... (remaining 14861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.94: 6611 22.94 - 45.87: 397 45.87 - 68.81: 33 68.81 - 91.75: 46 91.75 - 114.68: 45 Dihedral angle restraints: 7132 sinusoidal: 3367 harmonic: 3765 Sorted by residual: dihedral pdb=" CB CYS C 30 " pdb=" SG CYS C 30 " pdb=" SG CYS C 64 " pdb=" CB CYS C 64 " ideal model delta sinusoidal sigma weight residual 93.00 40.58 52.42 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS C 621 " pdb=" SG CYS C 621 " pdb=" SG CYS C 644 " pdb=" CB CYS C 644 " ideal model delta sinusoidal sigma weight residual -86.00 -39.45 -46.55 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA PHE C 284 " pdb=" C PHE C 284 " pdb=" N GLY C 285 " pdb=" CA GLY C 285 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1631 0.083 - 0.165: 183 0.165 - 0.248: 8 0.248 - 0.331: 7 0.331 - 0.414: 1 Chirality restraints: 1830 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 767 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1827 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 929 " -0.052 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO C 930 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 930 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 930 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 106 " 0.020 2.00e-02 2.50e+03 1.81e-02 4.11e+00 pdb=" CG ASN B 106 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 106 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 106 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG B1001 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 767 " 0.018 2.00e-02 2.50e+03 1.81e-02 4.10e+00 pdb=" CG ASN C 767 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 767 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 767 " -0.025 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.021 2.00e-02 2.50e+03 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1193 2.75 - 3.29: 10520 3.29 - 3.82: 16912 3.82 - 4.36: 21161 4.36 - 4.90: 35712 Nonbonded interactions: 85498 Sorted by model distance: nonbonded pdb=" NE2 GLN C 372 " pdb=" OD2 ASP C 394 " model vdw 2.211 2.520 nonbonded pdb=" O ASN C 468 " pdb=" ND2 ASN C 493 " model vdw 2.267 2.520 nonbonded pdb=" OE1 GLU A 136 " pdb=" OH TYR C 792 " model vdw 2.272 2.440 nonbonded pdb=" NE2 GLN C 911 " pdb=" OD1 ASP B 77 " model vdw 2.276 2.520 nonbonded pdb=" ND2 ASN A 84 " pdb=" OE1 GLU A 218 " model vdw 2.297 2.520 ... (remaining 85493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.420 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.420 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.005 0.057 10950 Z= 0.282 Angle : 0.736 8.601 14866 Z= 0.339 Chirality : 0.053 0.414 1830 Planarity : 0.004 0.078 1838 Dihedral : 18.084 114.683 4693 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.22), residues: 1298 helix: -2.70 (0.32), residues: 203 sheet: -2.74 (0.30), residues: 275 loop : -1.41 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 62 HIS 0.004 0.001 HIS C 292 PHE 0.016 0.001 PHE A 224 TYR 0.025 0.002 TYR A 108 ARG 0.003 0.000 ARG C 571 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8272 (p90) cc_final: 0.7637 (p90) REVERT: A 138 MET cc_start: 0.7923 (mmt) cc_final: 0.7697 (mmp) REVERT: C 59 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7136 (mm-30) REVERT: C 103 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7826 (ttmm) REVERT: C 123 GLU cc_start: 0.7235 (pp20) cc_final: 0.6925 (pp20) REVERT: C 353 MET cc_start: 0.7981 (mtp) cc_final: 0.7755 (mtm) REVERT: C 498 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7626 (ttmt) REVERT: C 544 SER cc_start: 0.8172 (p) cc_final: 0.7883 (p) REVERT: C 781 MET cc_start: 0.8037 (ttm) cc_final: 0.7663 (ttp) REVERT: C 813 TYR cc_start: 0.7879 (t80) cc_final: 0.7595 (t80) REVERT: C 831 VAL cc_start: 0.8207 (t) cc_final: 0.7969 (p) REVERT: C 881 MET cc_start: 0.7455 (ptp) cc_final: 0.7201 (ptp) REVERT: C 932 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7692 (mm-40) REVERT: B 105 ASN cc_start: 0.7697 (m-40) cc_final: 0.7205 (m-40) REVERT: B 123 SER cc_start: 0.8755 (t) cc_final: 0.8547 (t) REVERT: B 139 LEU cc_start: 0.8543 (tt) cc_final: 0.8201 (tp) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 1.0295 time to fit residues: 337.7172 Evaluate side-chains 277 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 51 GLN C 279 GLN C 322 ASN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 GLN C 923 ASN B 36 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 178 ASN B 199 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10950 Z= 0.288 Angle : 0.667 13.252 14866 Z= 0.318 Chirality : 0.050 0.232 1830 Planarity : 0.004 0.055 1838 Dihedral : 14.448 106.092 2295 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.64 % Allowed : 13.05 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.22), residues: 1298 helix: -2.64 (0.32), residues: 204 sheet: -2.76 (0.29), residues: 285 loop : -1.39 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.005 0.001 HIS C 292 PHE 0.020 0.002 PHE A 224 TYR 0.019 0.002 TYR C 533 ARG 0.011 0.000 ARG C 917 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 290 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8270 (p90) cc_final: 0.7608 (p90) REVERT: A 228 ASN cc_start: 0.8260 (t0) cc_final: 0.8044 (t0) REVERT: C 103 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7836 (ttmm) REVERT: C 123 GLU cc_start: 0.7331 (pp20) cc_final: 0.6964 (pp20) REVERT: C 300 ASN cc_start: 0.8067 (t0) cc_final: 0.7830 (t0) REVERT: C 373 LYS cc_start: 0.8436 (mttm) cc_final: 0.8232 (mttt) REVERT: C 498 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7612 (ttmt) REVERT: C 544 SER cc_start: 0.8138 (p) cc_final: 0.7857 (p) REVERT: C 610 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7885 (ttpt) REVERT: C 707 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7851 (mtpt) REVERT: C 711 ARG cc_start: 0.7636 (ttm-80) cc_final: 0.7274 (ttm-80) REVERT: C 764 CYS cc_start: 0.5889 (p) cc_final: 0.5650 (p) REVERT: C 781 MET cc_start: 0.8133 (ttm) cc_final: 0.7730 (ttp) REVERT: C 813 TYR cc_start: 0.7845 (t80) cc_final: 0.7631 (t80) REVERT: C 831 VAL cc_start: 0.8219 (t) cc_final: 0.7971 (p) REVERT: C 881 MET cc_start: 0.7446 (ptp) cc_final: 0.7203 (ptp) REVERT: C 932 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7704 (mm-40) REVERT: B 123 SER cc_start: 0.8798 (t) cc_final: 0.8578 (t) REVERT: B 139 LEU cc_start: 0.8650 (tt) cc_final: 0.8398 (tp) outliers start: 19 outliers final: 11 residues processed: 294 average time/residue: 1.0306 time to fit residues: 330.0768 Evaluate side-chains 291 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 280 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.0010 chunk 97 optimal weight: 0.0870 chunk 79 optimal weight: 0.0470 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 126 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN C 351 ASN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10950 Z= 0.141 Angle : 0.631 13.910 14866 Z= 0.296 Chirality : 0.059 1.463 1830 Planarity : 0.004 0.049 1838 Dihedral : 11.342 99.781 2295 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.73 % Allowed : 15.30 % Favored : 82.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.23), residues: 1298 helix: -2.53 (0.34), residues: 199 sheet: -2.82 (0.29), residues: 292 loop : -1.22 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 328 HIS 0.003 0.001 HIS C 292 PHE 0.010 0.001 PHE A 224 TYR 0.014 0.001 TYR C 533 ARG 0.012 0.000 ARG C 917 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 285 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8185 (p90) cc_final: 0.7634 (p90) REVERT: A 228 ASN cc_start: 0.8242 (t0) cc_final: 0.7986 (t0) REVERT: C 40 GLU cc_start: 0.7601 (tp30) cc_final: 0.7071 (tm-30) REVERT: C 59 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6770 (mm-30) REVERT: C 103 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7842 (ttmm) REVERT: C 123 GLU cc_start: 0.7365 (pp20) cc_final: 0.6991 (pp20) REVERT: C 128 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7484 (mm-30) REVERT: C 353 MET cc_start: 0.8107 (mtm) cc_final: 0.7685 (mtm) REVERT: C 498 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7604 (ttmt) REVERT: C 544 SER cc_start: 0.8145 (p) cc_final: 0.7855 (p) REVERT: C 625 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8437 (p) REVERT: C 711 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7255 (ttm-80) REVERT: C 768 PHE cc_start: 0.8680 (m-10) cc_final: 0.8435 (m-80) REVERT: C 781 MET cc_start: 0.8049 (ttm) cc_final: 0.7734 (ttp) REVERT: C 831 VAL cc_start: 0.8172 (t) cc_final: 0.7932 (p) REVERT: C 881 MET cc_start: 0.7437 (ptp) cc_final: 0.7195 (ptp) REVERT: C 932 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7681 (mm-40) REVERT: B 123 SER cc_start: 0.8785 (t) cc_final: 0.8563 (t) REVERT: B 139 LEU cc_start: 0.8697 (tt) cc_final: 0.8426 (tp) outliers start: 20 outliers final: 8 residues processed: 289 average time/residue: 0.9785 time to fit residues: 309.3452 Evaluate side-chains 294 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 284 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 901 HIS Chi-restraints excluded: chain B residue 106 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 GLN C 923 ASN B 93 GLN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10950 Z= 0.207 Angle : 0.619 9.735 14866 Z= 0.294 Chirality : 0.053 0.909 1830 Planarity : 0.004 0.059 1838 Dihedral : 9.970 90.385 2295 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.16 % Allowed : 16.68 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.23), residues: 1298 helix: -2.54 (0.34), residues: 199 sheet: -2.67 (0.29), residues: 291 loop : -1.25 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.004 0.001 HIS C 292 PHE 0.017 0.001 PHE A 224 TYR 0.017 0.001 TYR C 533 ARG 0.014 0.000 ARG C 917 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 288 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8235 (p90) cc_final: 0.7657 (p90) REVERT: C 59 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6757 (mm-30) REVERT: C 83 ASP cc_start: 0.7749 (p0) cc_final: 0.7453 (p0) REVERT: C 103 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7845 (ttmm) REVERT: C 187 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7891 (mt) REVERT: C 189 LEU cc_start: 0.8194 (tp) cc_final: 0.7978 (tm) REVERT: C 353 MET cc_start: 0.8166 (mtm) cc_final: 0.7693 (mtm) REVERT: C 498 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7614 (ttmt) REVERT: C 544 SER cc_start: 0.8119 (p) cc_final: 0.7833 (p) REVERT: C 625 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8428 (p) REVERT: C 674 ASN cc_start: 0.7722 (m110) cc_final: 0.7358 (m-40) REVERT: C 711 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7260 (ttm-80) REVERT: C 781 MET cc_start: 0.8130 (ttm) cc_final: 0.7840 (ttp) REVERT: C 831 VAL cc_start: 0.8191 (t) cc_final: 0.7951 (p) REVERT: C 881 MET cc_start: 0.7454 (ptp) cc_final: 0.7250 (ptp) REVERT: C 932 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7702 (mm-40) REVERT: B 123 SER cc_start: 0.8781 (t) cc_final: 0.8563 (t) outliers start: 25 outliers final: 16 residues processed: 294 average time/residue: 0.9562 time to fit residues: 308.1257 Evaluate side-chains 303 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 285 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 381 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 884 LYS Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10950 Z= 0.334 Angle : 0.659 9.918 14866 Z= 0.317 Chirality : 0.053 0.663 1830 Planarity : 0.004 0.069 1838 Dihedral : 9.549 85.790 2295 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.77 % Allowed : 17.46 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.22), residues: 1298 helix: -2.71 (0.32), residues: 211 sheet: -2.75 (0.29), residues: 289 loop : -1.36 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 28 HIS 0.006 0.001 HIS C 292 PHE 0.023 0.002 PHE A 224 TYR 0.018 0.002 TYR C 533 ARG 0.014 0.001 ARG C 917 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 289 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8424 (mp10) REVERT: C 59 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6765 (mm-30) REVERT: C 83 ASP cc_start: 0.7685 (p0) cc_final: 0.7407 (p0) REVERT: C 103 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7863 (ttmm) REVERT: C 123 GLU cc_start: 0.7440 (pp20) cc_final: 0.6985 (pp20) REVERT: C 189 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8073 (tm) REVERT: C 373 LYS cc_start: 0.8446 (mttm) cc_final: 0.8229 (mttt) REVERT: C 498 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7591 (ttmt) REVERT: C 544 SER cc_start: 0.8159 (p) cc_final: 0.7861 (p) REVERT: C 674 ASN cc_start: 0.7710 (m110) cc_final: 0.7382 (m-40) REVERT: C 711 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7296 (ttm-80) REVERT: C 781 MET cc_start: 0.8198 (ttm) cc_final: 0.7915 (ttp) REVERT: C 831 VAL cc_start: 0.8228 (t) cc_final: 0.7976 (p) REVERT: C 881 MET cc_start: 0.7460 (ptp) cc_final: 0.7248 (ptp) REVERT: C 932 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7729 (mm-40) REVERT: B 123 SER cc_start: 0.8738 (t) cc_final: 0.8496 (t) REVERT: B 129 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7906 (t0) outliers start: 32 outliers final: 20 residues processed: 298 average time/residue: 0.9946 time to fit residues: 323.5804 Evaluate side-chains 306 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 283 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 381 MET Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 884 LYS Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 279 GLN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN B 36 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10950 Z= 0.324 Angle : 0.652 10.116 14866 Z= 0.316 Chirality : 0.052 0.547 1830 Planarity : 0.004 0.071 1838 Dihedral : 9.062 82.882 2295 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.03 % Allowed : 17.98 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.22), residues: 1298 helix: -2.74 (0.32), residues: 209 sheet: -2.68 (0.30), residues: 273 loop : -1.48 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 28 HIS 0.005 0.001 HIS C 292 PHE 0.024 0.002 PHE A 224 TYR 0.017 0.002 TYR C 533 ARG 0.015 0.000 ARG C 917 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 286 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.8148 (t80) REVERT: C 59 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6775 (mm-30) REVERT: C 83 ASP cc_start: 0.7627 (p0) cc_final: 0.7361 (p0) REVERT: C 103 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7864 (ttmm) REVERT: C 123 GLU cc_start: 0.7426 (pp20) cc_final: 0.6984 (pp20) REVERT: C 189 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8043 (tm) REVERT: C 353 MET cc_start: 0.8180 (mtm) cc_final: 0.7846 (mtm) REVERT: C 373 LYS cc_start: 0.8443 (mttm) cc_final: 0.8230 (mttt) REVERT: C 498 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7592 (ttmt) REVERT: C 544 SER cc_start: 0.8157 (p) cc_final: 0.7862 (p) REVERT: C 674 ASN cc_start: 0.7740 (m110) cc_final: 0.7440 (m-40) REVERT: C 711 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7307 (ttm-80) REVERT: C 768 PHE cc_start: 0.8736 (m-10) cc_final: 0.8531 (m-80) REVERT: C 781 MET cc_start: 0.8214 (ttm) cc_final: 0.7932 (ttp) REVERT: C 881 MET cc_start: 0.7462 (ptp) cc_final: 0.7244 (ptp) REVERT: C 932 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7732 (mm-40) REVERT: B 123 SER cc_start: 0.8675 (t) cc_final: 0.8433 (t) REVERT: B 129 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7772 (t0) REVERT: B 130 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7396 (mtm-85) outliers start: 35 outliers final: 18 residues processed: 301 average time/residue: 0.8808 time to fit residues: 290.7177 Evaluate side-chains 307 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 285 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.0670 chunk 71 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.0050 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.0000 chunk 76 optimal weight: 0.8980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 GLN C 923 ASN B 36 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10950 Z= 0.140 Angle : 0.599 9.845 14866 Z= 0.286 Chirality : 0.049 0.477 1830 Planarity : 0.004 0.070 1838 Dihedral : 8.455 79.931 2295 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.07 % Allowed : 19.79 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.23), residues: 1298 helix: -2.53 (0.34), residues: 197 sheet: -2.55 (0.29), residues: 305 loop : -1.21 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 328 HIS 0.002 0.001 HIS C 292 PHE 0.010 0.001 PHE A 224 TYR 0.013 0.001 TYR C 533 ARG 0.017 0.000 ARG C 917 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 294 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8234 (p90) cc_final: 0.7699 (p90) REVERT: A 108 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 138 MET cc_start: 0.8307 (mtp) cc_final: 0.8002 (mtm) REVERT: C 40 GLU cc_start: 0.7568 (tp30) cc_final: 0.7029 (tm-30) REVERT: C 59 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6740 (mm-30) REVERT: C 83 ASP cc_start: 0.7624 (p0) cc_final: 0.7386 (p0) REVERT: C 103 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7870 (ttmm) REVERT: C 123 GLU cc_start: 0.7397 (pp20) cc_final: 0.6935 (pp20) REVERT: C 333 PHE cc_start: 0.8682 (m-10) cc_final: 0.8422 (m-80) REVERT: C 498 LYS cc_start: 0.7876 (ttmt) cc_final: 0.7565 (ttmt) REVERT: C 544 SER cc_start: 0.8140 (p) cc_final: 0.7865 (p) REVERT: C 674 ASN cc_start: 0.7667 (m110) cc_final: 0.7383 (m-40) REVERT: C 711 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7269 (ttm-80) REVERT: C 770 LEU cc_start: 0.8415 (mp) cc_final: 0.8149 (mt) REVERT: C 781 MET cc_start: 0.8140 (ttm) cc_final: 0.7675 (ttp) REVERT: C 831 VAL cc_start: 0.8181 (t) cc_final: 0.7948 (p) REVERT: C 841 MET cc_start: 0.8404 (mtp) cc_final: 0.8109 (mtm) REVERT: C 865 MET cc_start: 0.8353 (mtp) cc_final: 0.8133 (mtm) REVERT: C 881 MET cc_start: 0.7445 (ptp) cc_final: 0.7236 (ptp) REVERT: B 123 SER cc_start: 0.8735 (t) cc_final: 0.8512 (t) REVERT: B 130 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7353 (mtm-85) outliers start: 24 outliers final: 13 residues processed: 303 average time/residue: 0.9648 time to fit residues: 319.6281 Evaluate side-chains 300 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 285 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.5980 chunk 74 optimal weight: 0.0670 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 279 GLN C 351 ASN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10950 Z= 0.164 Angle : 0.602 9.858 14866 Z= 0.288 Chirality : 0.048 0.439 1830 Planarity : 0.004 0.077 1838 Dihedral : 8.165 76.250 2295 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.82 % Allowed : 20.31 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.23), residues: 1298 helix: -2.57 (0.33), residues: 207 sheet: -2.55 (0.29), residues: 307 loop : -1.18 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 62 HIS 0.003 0.001 HIS C 292 PHE 0.013 0.001 PHE A 224 TYR 0.014 0.001 TYR C 533 ARG 0.018 0.000 ARG C 917 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 286 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8229 (p90) cc_final: 0.7703 (p90) REVERT: A 77 THR cc_start: 0.8643 (p) cc_final: 0.8068 (t) REVERT: A 108 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.8136 (t80) REVERT: A 138 MET cc_start: 0.8296 (mtp) cc_final: 0.8029 (mtm) REVERT: C 40 GLU cc_start: 0.7561 (tp30) cc_final: 0.7028 (tm-30) REVERT: C 59 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6747 (mm-30) REVERT: C 103 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7870 (ttmm) REVERT: C 123 GLU cc_start: 0.7280 (pp20) cc_final: 0.6923 (pp20) REVERT: C 333 PHE cc_start: 0.8692 (m-10) cc_final: 0.8431 (m-80) REVERT: C 498 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7580 (ttmt) REVERT: C 544 SER cc_start: 0.8115 (p) cc_final: 0.7829 (p) REVERT: C 674 ASN cc_start: 0.7667 (m110) cc_final: 0.7399 (m-40) REVERT: C 711 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7251 (ttm-80) REVERT: C 781 MET cc_start: 0.8166 (ttm) cc_final: 0.7743 (ttp) REVERT: C 831 VAL cc_start: 0.8154 (t) cc_final: 0.7926 (p) REVERT: C 841 MET cc_start: 0.8433 (mtp) cc_final: 0.8208 (mtm) REVERT: C 865 MET cc_start: 0.8402 (mtp) cc_final: 0.8193 (mtm) REVERT: C 881 MET cc_start: 0.7435 (ptp) cc_final: 0.7234 (ptp) REVERT: B 123 SER cc_start: 0.8737 (t) cc_final: 0.8514 (t) REVERT: B 130 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7248 (mtm-85) outliers start: 21 outliers final: 14 residues processed: 293 average time/residue: 0.9654 time to fit residues: 308.6712 Evaluate side-chains 296 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 280 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 884 LYS Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 GLN C 923 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 10950 Z= 0.224 Angle : 0.624 9.908 14866 Z= 0.301 Chirality : 0.049 0.419 1830 Planarity : 0.004 0.083 1838 Dihedral : 8.081 73.241 2295 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.38 % Allowed : 20.74 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.23), residues: 1298 helix: -2.60 (0.32), residues: 207 sheet: -2.53 (0.29), residues: 306 loop : -1.22 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 62 HIS 0.004 0.001 HIS C 292 PHE 0.017 0.001 PHE A 224 TYR 0.016 0.001 TYR C 533 ARG 0.019 0.000 ARG C 917 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 285 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8244 (p90) cc_final: 0.7695 (p90) REVERT: A 77 THR cc_start: 0.8648 (p) cc_final: 0.8072 (t) REVERT: A 108 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8088 (t80) REVERT: C 40 GLU cc_start: 0.7566 (tp30) cc_final: 0.7033 (tm-30) REVERT: C 59 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6748 (mm-30) REVERT: C 76 THR cc_start: 0.8409 (m) cc_final: 0.8151 (t) REVERT: C 103 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7859 (ttmm) REVERT: C 123 GLU cc_start: 0.7258 (pp20) cc_final: 0.6929 (pp20) REVERT: C 333 PHE cc_start: 0.8700 (m-10) cc_final: 0.8430 (m-80) REVERT: C 498 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7586 (ttmt) REVERT: C 544 SER cc_start: 0.8122 (p) cc_final: 0.7838 (p) REVERT: C 674 ASN cc_start: 0.7682 (m110) cc_final: 0.7423 (m-40) REVERT: C 711 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7252 (ttm-80) REVERT: C 781 MET cc_start: 0.8202 (ttm) cc_final: 0.7832 (ttp) REVERT: C 831 VAL cc_start: 0.8190 (t) cc_final: 0.7964 (p) REVERT: C 841 MET cc_start: 0.8439 (mtp) cc_final: 0.8218 (mtm) REVERT: C 865 MET cc_start: 0.8410 (mtp) cc_final: 0.8204 (mtm) REVERT: C 881 MET cc_start: 0.7441 (ptp) cc_final: 0.7230 (ptp) REVERT: B 123 SER cc_start: 0.8688 (t) cc_final: 0.8461 (t) REVERT: B 130 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7225 (mtm-85) outliers start: 16 outliers final: 12 residues processed: 290 average time/residue: 0.9256 time to fit residues: 293.5829 Evaluate side-chains 298 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 284 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 279 GLN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN B 86 GLN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10950 Z= 0.187 Angle : 0.609 9.817 14866 Z= 0.292 Chirality : 0.048 0.398 1830 Planarity : 0.004 0.083 1838 Dihedral : 7.792 69.575 2295 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.47 % Allowed : 21.00 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.23), residues: 1298 helix: -2.56 (0.33), residues: 205 sheet: -2.48 (0.29), residues: 304 loop : -1.21 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 62 HIS 0.003 0.001 HIS C 292 PHE 0.014 0.001 PHE A 224 TYR 0.014 0.001 TYR C 533 ARG 0.019 0.000 ARG C 917 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 291 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8230 (p90) cc_final: 0.7689 (p90) REVERT: A 77 THR cc_start: 0.8635 (p) cc_final: 0.8061 (t) REVERT: A 108 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8077 (t80) REVERT: A 138 MET cc_start: 0.8315 (mtp) cc_final: 0.8108 (mtm) REVERT: C 40 GLU cc_start: 0.7562 (tp30) cc_final: 0.7030 (tm-30) REVERT: C 76 THR cc_start: 0.8363 (m) cc_final: 0.8097 (t) REVERT: C 103 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7869 (ttmm) REVERT: C 123 GLU cc_start: 0.7302 (pp20) cc_final: 0.6971 (pp20) REVERT: C 333 PHE cc_start: 0.8683 (m-10) cc_final: 0.8393 (m-80) REVERT: C 498 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7573 (ttmt) REVERT: C 544 SER cc_start: 0.8131 (p) cc_final: 0.7860 (p) REVERT: C 625 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8427 (p) REVERT: C 674 ASN cc_start: 0.7676 (m110) cc_final: 0.7421 (m-40) REVERT: C 711 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7236 (ttm-80) REVERT: C 781 MET cc_start: 0.8194 (ttm) cc_final: 0.7723 (ttp) REVERT: C 831 VAL cc_start: 0.8132 (t) cc_final: 0.7906 (p) REVERT: C 841 MET cc_start: 0.8439 (mtp) cc_final: 0.8220 (mtm) REVERT: C 865 MET cc_start: 0.8399 (mtp) cc_final: 0.8167 (mtm) REVERT: B 123 SER cc_start: 0.8727 (t) cc_final: 0.8504 (t) REVERT: B 130 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7034 (mtm-85) outliers start: 17 outliers final: 13 residues processed: 297 average time/residue: 0.9306 time to fit residues: 302.2609 Evaluate side-chains 302 residues out of total 1157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 286 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN C 351 ASN C 456 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 GLN C 815 ASN C 923 ASN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096200 restraints weight = 16325.607| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.38 r_work: 0.3138 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10950 Z= 0.229 Angle : 0.629 9.901 14866 Z= 0.304 Chirality : 0.049 0.385 1830 Planarity : 0.004 0.086 1838 Dihedral : 7.754 66.051 2295 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.38 % Allowed : 21.26 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.23), residues: 1298 helix: -2.65 (0.32), residues: 213 sheet: -2.51 (0.29), residues: 306 loop : -1.23 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 62 HIS 0.004 0.001 HIS C 292 PHE 0.018 0.001 PHE A 224 TYR 0.019 0.001 TYR A 37 ARG 0.019 0.000 ARG C 917 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5048.68 seconds wall clock time: 100 minutes 6.68 seconds (6006.68 seconds total)