Starting phenix.real_space_refine on Fri Mar 15 20:46:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyx_12657/03_2024/7nyx_12657_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyx_12657/03_2024/7nyx_12657.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyx_12657/03_2024/7nyx_12657_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyx_12657/03_2024/7nyx_12657_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyx_12657/03_2024/7nyx_12657_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyx_12657/03_2024/7nyx_12657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyx_12657/03_2024/7nyx_12657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyx_12657/03_2024/7nyx_12657_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyx_12657/03_2024/7nyx_12657_trim_updated.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 111 5.49 5 Mg 2 5.21 5 S 121 5.16 5 C 22081 2.51 5 N 6548 2.21 5 O 7233 1.98 5 H 34688 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1457": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "J TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 70784 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 23552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1467, 23552 Classifications: {'peptide': 1467} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1434} Chain: "B" Number of atoms: 23552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1467, 23552 Classifications: {'peptide': 1467} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1434} Chain: "C" Number of atoms: 5330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5330 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 327} Chain breaks: 1 Chain: "D" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1469 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3441 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3246 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "G" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1105 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1105 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "I" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2272 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "J" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2288 Classifications: {'peptide': 135} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "K" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 694 Classifications: {'DNA': 22} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 21} Chain: "L" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 702 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "M" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 961 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 961 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 22.23, per 1000 atoms: 0.31 Number of scatterers: 70784 At special positions: 0 Unit cell: (200.594, 261.644, 267.459, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 121 16.00 P 111 15.00 Mg 2 11.99 O 7233 8.00 N 6548 7.00 C 22081 6.00 H 34688 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 45.42 Conformation dependent library (CDL) restraints added in 5.2 seconds 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 13 sheets defined 66.4% alpha, 5.3% beta 52 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 30.39 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 226 through 400 removed outlier: 3.882A pdb=" N HIS A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 407 through 429 Processing helix chain 'A' and resid 440 through 469 removed outlier: 3.645A pdb=" N ASP A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 486 Processing helix chain 'A' and resid 491 through 545 removed outlier: 4.021A pdb=" N TRP A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLN A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Proline residue: A 506 - end of helix removed outlier: 3.971A pdb=" N ASP A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG A 514 " --> pdb=" O HIS A 510 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Proline residue: A 517 - end of helix removed outlier: 3.957A pdb=" N LYS A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 617 removed outlier: 3.826A pdb=" N ASN A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Proline residue: A 602 - end of helix Processing helix chain 'A' and resid 625 through 661 Processing helix chain 'A' and resid 672 through 680 Processing helix chain 'A' and resid 686 through 690 Processing helix chain 'A' and resid 695 through 709 Proline residue: A 699 - end of helix Proline residue: A 707 - end of helix Processing helix chain 'A' and resid 718 through 724 Proline residue: A 722 - end of helix No H-bonds generated for 'chain 'A' and resid 718 through 724' Processing helix chain 'A' and resid 784 through 824 Processing helix chain 'A' and resid 835 through 879 Processing helix chain 'A' and resid 884 through 887 No H-bonds generated for 'chain 'A' and resid 884 through 887' Processing helix chain 'A' and resid 895 through 930 removed outlier: 5.617A pdb=" N SER A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Proline residue: A 924 - end of helix removed outlier: 6.184A pdb=" N ALA A 927 " --> pdb=" O GLU A 923 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL A 928 " --> pdb=" O PRO A 924 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN A 930 " --> pdb=" O VAL A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 981 removed outlier: 3.532A pdb=" N GLU A 937 " --> pdb=" O PRO A 933 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL A 968 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N HIS A 969 " --> pdb=" O GLN A 965 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 971 " --> pdb=" O ARG A 967 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 973 " --> pdb=" O HIS A 969 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A 975 " --> pdb=" O SER A 971 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 981 " --> pdb=" O GLY A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1045 Processing helix chain 'A' and resid 1051 through 1124 removed outlier: 3.761A pdb=" N ASN A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A1119 " --> pdb=" O ALA A1115 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 3.911A pdb=" N TYR A1140 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1160 removed outlier: 3.641A pdb=" N LEU A1159 " --> pdb=" O GLY A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1173 Processing helix chain 'A' and resid 1180 through 1198 removed outlier: 3.879A pdb=" N GLN A1192 " --> pdb=" O ALA A1189 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG A1197 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1262 removed outlier: 3.845A pdb=" N ILE A1212 " --> pdb=" O VAL A1209 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A1213 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1292 removed outlier: 3.958A pdb=" N LEU A1286 " --> pdb=" O SER A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1300 No H-bonds generated for 'chain 'A' and resid 1298 through 1300' Processing helix chain 'A' and resid 1308 through 1318 Processing helix chain 'A' and resid 1330 through 1337 Processing helix chain 'A' and resid 1341 through 1343 No H-bonds generated for 'chain 'A' and resid 1341 through 1343' Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1367 through 1392 removed outlier: 4.523A pdb=" N ARG A1391 " --> pdb=" O GLU A1387 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU A1392 " --> pdb=" O GLU A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1410 No H-bonds generated for 'chain 'A' and resid 1408 through 1410' Processing helix chain 'A' and resid 1413 through 1425 Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 191 through 206 Processing helix chain 'B' and resid 211 through 221 removed outlier: 5.770A pdb=" N ARG B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP B 219 " --> pdb=" O ARG B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 408 removed outlier: 3.718A pdb=" N ALA B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP B 273 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 303 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU B 406 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 Processing helix chain 'B' and resid 440 through 486 removed outlier: 3.524A pdb=" N LYS B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 545 Proline residue: B 506 - end of helix removed outlier: 3.890A pdb=" N ARG B 514 " --> pdb=" O HIS B 510 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLN B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Proline residue: B 517 - end of helix Processing helix chain 'B' and resid 556 through 617 Proline residue: B 602 - end of helix Processing helix chain 'B' and resid 625 through 663 removed outlier: 3.738A pdb=" N VAL B 644 " --> pdb=" O ARG B 640 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 663 " --> pdb=" O GLN B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.752A pdb=" N ILE B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA B 676 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 689 No H-bonds generated for 'chain 'B' and resid 686 through 689' Processing helix chain 'B' and resid 695 through 708 Proline residue: B 699 - end of helix Proline residue: B 707 - end of helix Processing helix chain 'B' and resid 719 through 726 removed outlier: 4.267A pdb=" N HIS B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU B 725 " --> pdb=" O ARG B 721 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 726 " --> pdb=" O PRO B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 828 removed outlier: 3.876A pdb=" N ALA B 796 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 797 " --> pdb=" O GLU B 793 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 827 " --> pdb=" O GLY B 823 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 828 " --> pdb=" O LYS B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 879 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 895 through 923 removed outlier: 5.467A pdb=" N SER B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ALA B 918 " --> pdb=" O GLN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 930 Processing helix chain 'B' and resid 934 through 972 removed outlier: 4.732A pdb=" N VAL B 968 " --> pdb=" O VAL B 964 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N HIS B 969 " --> pdb=" O GLN B 965 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 972 " --> pdb=" O VAL B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1045 Processing helix chain 'B' and resid 1051 through 1124 removed outlier: 3.705A pdb=" N LYS B1095 " --> pdb=" O ASN B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1140 removed outlier: 4.001A pdb=" N TYR B1140 " --> pdb=" O GLU B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1161 removed outlier: 3.608A pdb=" N LEU B1159 " --> pdb=" O GLY B1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1175 removed outlier: 3.855A pdb=" N GLU B1175 " --> pdb=" O LEU B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1194 Processing helix chain 'B' and resid 1201 through 1203 No H-bonds generated for 'chain 'B' and resid 1201 through 1203' Processing helix chain 'B' and resid 1208 through 1261 removed outlier: 3.689A pdb=" N ILE B1212 " --> pdb=" O PRO B1208 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU B1213 " --> pdb=" O VAL B1209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN B1214 " --> pdb=" O ASP B1210 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B1260 " --> pdb=" O ARG B1256 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY B1261 " --> pdb=" O MET B1257 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1292 removed outlier: 3.906A pdb=" N LEU B1286 " --> pdb=" O SER B1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 1295 through 1301 removed outlier: 5.135A pdb=" N ASP B1299 " --> pdb=" O GLN B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1318 Processing helix chain 'B' and resid 1330 through 1338 Processing helix chain 'B' and resid 1340 through 1343 Processing helix chain 'B' and resid 1362 through 1364 No H-bonds generated for 'chain 'B' and resid 1362 through 1364' Processing helix chain 'B' and resid 1367 through 1390 Processing helix chain 'B' and resid 1408 through 1410 No H-bonds generated for 'chain 'B' and resid 1408 through 1410' Processing helix chain 'B' and resid 1413 through 1425 Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 122 through 145 Processing helix chain 'C' and resid 149 through 156 Processing helix chain 'C' and resid 159 through 196 Processing helix chain 'C' and resid 201 through 223 Processing helix chain 'C' and resid 226 through 242 removed outlier: 4.082A pdb=" N MET C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLY C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 287 removed outlier: 4.309A pdb=" N GLN C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 308 through 311 Processing helix chain 'C' and resid 354 through 372 removed outlier: 4.421A pdb=" N VAL C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 388 removed outlier: 3.868A pdb=" N ALA C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLN C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.460A pdb=" N PHE C 395 " --> pdb=" O PRO C 392 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 Processing helix chain 'D' and resid 26 through 41 Processing helix chain 'D' and resid 49 through 63 removed outlier: 3.760A pdb=" N ASP D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 105 through 114 removed outlier: 4.098A pdb=" N TYR D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 12 through 18 Processing helix chain 'E' and resid 23 through 31 Processing helix chain 'E' and resid 41 through 49 Processing helix chain 'E' and resid 51 through 61 removed outlier: 3.829A pdb=" N ARG E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR E 61 " --> pdb=" O PHE E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 104 Processing helix chain 'E' and resid 109 through 111 No H-bonds generated for 'chain 'E' and resid 109 through 111' Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 130 through 137 removed outlier: 4.318A pdb=" N PHE E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 165 Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'E' and resid 197 through 207 removed outlier: 3.685A pdb=" N LEU E 202 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 19 Processing helix chain 'F' and resid 23 through 31 Processing helix chain 'F' and resid 41 through 59 removed outlier: 5.573A pdb=" N GLU F 52 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 145 through 165 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'F' and resid 197 through 205 Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.848A pdb=" N LYS G 8 " --> pdb=" O GLU G 5 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE G 11 " --> pdb=" O LYS G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 31 No H-bonds generated for 'chain 'G' and resid 28 through 31' Processing helix chain 'G' and resid 36 through 49 Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.974A pdb=" N LYS G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 70 Processing helix chain 'H' and resid 3 through 15 removed outlier: 4.260A pdb=" N LYS H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 50 removed outlier: 3.543A pdb=" N PHE H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'I' and resid 7 through 23 removed outlier: 3.896A pdb=" N GLY I 12 " --> pdb=" O ASN I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 47 Processing helix chain 'I' and resid 51 through 61 removed outlier: 3.948A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 85 removed outlier: 3.512A pdb=" N PHE I 67 " --> pdb=" O PRO I 64 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN I 68 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA I 84 " --> pdb=" O HIS I 81 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 111 Processing helix chain 'I' and resid 115 through 133 Processing helix chain 'J' and resid 7 through 23 removed outlier: 3.900A pdb=" N GLY J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 49 removed outlier: 3.759A pdb=" N GLU J 48 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N SER J 49 " --> pdb=" O ILE J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 61 removed outlier: 3.590A pdb=" N HIS J 61 " --> pdb=" O ILE J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 85 removed outlier: 3.837A pdb=" N PHE J 67 " --> pdb=" O PRO J 64 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN J 68 " --> pdb=" O ASP J 65 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE J 74 " --> pdb=" O LYS J 71 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA J 84 " --> pdb=" O HIS J 81 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU J 85 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 89 No H-bonds generated for 'chain 'J' and resid 87 through 89' Processing helix chain 'J' and resid 98 through 111 Processing helix chain 'J' and resid 115 through 134 Processing sheet with id= A, first strand: chain 'A' and resid 20 through 24 removed outlier: 6.779A pdb=" N ASP A 91 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A 10 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 89 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 12 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 87 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS A 115 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1456 through 1464 removed outlier: 6.207A pdb=" N LEU A1430 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU A 32 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A1432 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 751 through 754 removed outlier: 7.035A pdb=" N GLN A 766 " --> pdb=" O SER A 762 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1273 through 1279 Processing sheet with id= E, first strand: chain 'B' and resid 20 through 24 removed outlier: 6.951A pdb=" N ASP B 91 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU B 10 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 89 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 12 " --> pdb=" O TYR B 87 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR B 87 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1456 through 1463 removed outlier: 6.419A pdb=" N LEU B1430 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 32 " --> pdb=" O LEU B1430 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B1432 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 751 through 754 removed outlier: 6.940A pdb=" N GLN B 766 " --> pdb=" O SER B 762 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 1273 through 1279 Processing sheet with id= I, first strand: chain 'D' and resid 87 through 90 Processing sheet with id= J, first strand: chain 'E' and resid 63 through 67 Processing sheet with id= K, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= L, first strand: chain 'F' and resid 63 through 67 Processing sheet with id= M, first strand: chain 'F' and resid 168 through 170 2215 hydrogen bonds defined for protein. 6159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 26.02 Time building geometry restraints manager: 47.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 34656 1.03 - 1.23: 133 1.23 - 1.42: 15540 1.42 - 1.62: 20986 1.62 - 1.82: 216 Bond restraints: 71531 Sorted by residual: bond pdb=" NE2 GLN B1407 " pdb="HE22 GLN B1407 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" NE2 HIS A 309 " pdb=" HE2 HIS A 309 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" NE2 GLN A1407 " pdb="HE22 GLN A1407 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" NE2 GLN A1407 " pdb="HE21 GLN A1407 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" NE2 HIS B 915 " pdb=" HE2 HIS B 915 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.61e+01 ... (remaining 71526 not shown) Histogram of bond angle deviations from ideal: 59.63 - 75.66: 6 75.66 - 91.69: 2 91.69 - 107.72: 6299 107.72 - 123.74: 117019 123.74 - 139.77: 5663 Bond angle restraints: 128989 Sorted by residual: angle pdb=" C GLU B1088 " pdb=" N MET B1089 " pdb=" H MET B1089 " ideal model delta sigma weight residual 125.01 69.80 55.21 3.00e+00 1.11e-01 3.39e+02 angle pdb=" CA MET B1089 " pdb=" N MET B1089 " pdb=" H MET B1089 " ideal model delta sigma weight residual 114.71 59.63 55.08 3.00e+00 1.11e-01 3.37e+02 angle pdb=" C SER F 144 " pdb=" CA SER F 144 " pdb=" HA SER F 144 " ideal model delta sigma weight residual 109.00 73.63 35.37 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB THR A 304 " pdb=" CA THR A 304 " pdb=" HA THR A 304 " ideal model delta sigma weight residual 109.00 74.09 34.91 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C THR A 304 " pdb=" CA THR A 304 " pdb=" HA THR A 304 " ideal model delta sigma weight residual 109.00 74.58 34.42 3.00e+00 1.11e-01 1.32e+02 ... (remaining 128984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 28859 17.95 - 35.91: 2806 35.91 - 53.86: 957 53.86 - 71.81: 295 71.81 - 89.77: 54 Dihedral angle restraints: 32971 sinusoidal: 19074 harmonic: 13897 Sorted by residual: dihedral pdb=" CA LYS B 824 " pdb=" C LYS B 824 " pdb=" N HIS B 825 " pdb=" CA HIS B 825 " ideal model delta harmonic sigma weight residual 180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ARG B 548 " pdb=" C ARG B 548 " pdb=" N GLN B 549 " pdb=" CA GLN B 549 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ARG A 548 " pdb=" C ARG A 548 " pdb=" N GLN A 549 " pdb=" CA GLN A 549 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 32968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5083 0.072 - 0.143: 419 0.143 - 0.215: 18 0.215 - 0.286: 5 0.286 - 0.358: 5 Chirality restraints: 5530 Sorted by residual: chirality pdb=" CA THR A 304 " pdb=" N THR A 304 " pdb=" C THR A 304 " pdb=" CB THR A 304 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA SER F 144 " pdb=" N SER F 144 " pdb=" C SER F 144 " pdb=" CB SER F 144 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA PRO F 106 " pdb=" N PRO F 106 " pdb=" C PRO F 106 " pdb=" CB PRO F 106 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 5527 not shown) Planarity restraints: 10428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 105 " 0.122 5.00e-02 4.00e+02 1.76e-01 4.96e+01 pdb=" N PRO F 106 " -0.304 5.00e-02 4.00e+02 pdb=" CA PRO F 106 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO F 106 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C38 PNS H 101 " -0.054 2.00e-02 2.50e+03 5.76e-02 4.15e+01 pdb=" C39 PNS H 101 " 0.022 2.00e-02 2.50e+03 pdb=" C42 PNS H 101 " -0.070 2.00e-02 2.50e+03 pdb=" N41 PNS H 101 " 0.091 2.00e-02 2.50e+03 pdb=" O40 PNS H 101 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 51 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLN E 51 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN E 51 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU E 52 " -0.021 2.00e-02 2.50e+03 ... (remaining 10425 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 723 1.98 - 2.63: 92969 2.63 - 3.29: 219704 3.29 - 3.94: 270377 3.94 - 4.60: 421282 Nonbonded interactions: 1005055 Sorted by model distance: nonbonded pdb="HE21 GLN A1407 " pdb=" HG1 THR B1367 " model vdw 1.322 2.100 nonbonded pdb=" HG1 THR A1367 " pdb="HE21 GLN B1407 " model vdw 1.397 2.100 nonbonded pdb=" H LEU J 115 " pdb=" OP1 DA K 67 " model vdw 1.479 1.850 nonbonded pdb=" OE2 GLU A 359 " pdb="HH11 ARG A 363 " model vdw 1.515 1.850 nonbonded pdb=" O ALA B 607 " pdb=" HE2 HIS B 825 " model vdw 1.515 1.850 ... (remaining 1005050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 79 through 308 or (resid 309 and (name N or name CA or name C or na \ me O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or na \ me H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or \ resid 310 through 994 or (resid 995 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resi \ d 996 through 1468)) selection = (chain 'B' and (resid 2 through 276 or (resid 277 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 278 through 824 or (resid 825 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 826 through 914 or (resid 915 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or r \ esid 916 through 1468)) } ncs_group { reference = (chain 'E' and resid 9 through 206) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 62 through 134)) selection = (chain 'J' and resid 1 through 134) } ncs_group { reference = chain 'M' selection = chain 'N' } 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 group one per residue 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: 1.320 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: 0.760 Extract box with map and model: 9.050 Check model and map are aligned: 0.780 Set scattering table: 0.500 Process input model: 195.000 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.003 0.126 36843 Z= 0.210 Angle : 0.605 16.364 50130 Z= 0.344 Chirality : 0.039 0.358 5530 Planarity : 0.004 0.176 6291 Dihedral : 17.456 89.768 14551 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.13), residues: 4164 helix: 2.08 (0.10), residues: 2717 sheet: -0.13 (0.31), residues: 269 loop : -0.74 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 15 HIS 0.013 0.001 HIS B 845 PHE 0.057 0.001 PHE B 47 TYR 0.018 0.001 TYR B 174 ARG 0.011 0.001 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 4.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.9126 (mmp) cc_final: 0.8534 (mmp) REVERT: A 1375 MET cc_start: 0.8764 (mmm) cc_final: 0.8558 (mmm) REVERT: B 122 MET cc_start: 0.8040 (ttp) cc_final: 0.7538 (ptm) REVERT: B 205 LEU cc_start: 0.9584 (tp) cc_final: 0.9345 (tt) REVERT: B 344 MET cc_start: 0.7770 (mmp) cc_final: 0.7154 (mmm) REVERT: B 1215 MET cc_start: 0.9349 (mtp) cc_final: 0.9077 (mtp) REVERT: C 173 MET cc_start: 0.9837 (mmm) cc_final: 0.9482 (mmm) REVERT: D 33 MET cc_start: 0.9613 (mmm) cc_final: 0.9289 (mmm) REVERT: D 47 MET cc_start: 0.8065 (mmm) cc_final: 0.7823 (tpp) REVERT: D 96 ASP cc_start: 0.9164 (t70) cc_final: 0.8899 (t0) REVERT: E 93 MET cc_start: 0.9129 (mmt) cc_final: 0.8508 (mmm) REVERT: E 94 MET cc_start: 0.9603 (mmp) cc_final: 0.9359 (mmm) REVERT: E 103 TYR cc_start: 0.9414 (t80) cc_final: 0.9158 (t80) REVERT: E 169 TYR cc_start: 0.7507 (m-10) cc_final: 0.7303 (m-10) REVERT: E 204 MET cc_start: 0.9363 (mtm) cc_final: 0.8835 (mmp) REVERT: E 211 MET cc_start: 0.8303 (mmp) cc_final: 0.8094 (mmp) REVERT: F 199 GLU cc_start: 0.9419 (tp30) cc_final: 0.9181 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.9308 time to fit residues: 297.1294 Evaluate side-chains 156 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 9.9990 chunk 321 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 385 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 815 HIS ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS C 371 GLN D 84 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36843 Z= 0.356 Angle : 0.596 9.408 50130 Z= 0.353 Chirality : 0.038 0.358 5530 Planarity : 0.004 0.076 6291 Dihedral : 15.040 88.548 5930 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.13), residues: 4164 helix: 1.51 (0.10), residues: 2734 sheet: -0.54 (0.30), residues: 271 loop : -0.87 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 15 HIS 0.008 0.001 HIS B 330 PHE 0.021 0.002 PHE B 47 TYR 0.016 0.002 TYR B 307 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1149 MET cc_start: 0.8762 (ptp) cc_final: 0.8346 (ptp) REVERT: A 1375 MET cc_start: 0.8941 (mmm) cc_final: 0.8703 (mmm) REVERT: B 122 MET cc_start: 0.8102 (ttp) cc_final: 0.7612 (ptm) REVERT: B 205 LEU cc_start: 0.9587 (tp) cc_final: 0.9338 (tt) REVERT: B 1215 MET cc_start: 0.9392 (mtp) cc_final: 0.9108 (mtp) REVERT: B 1403 LEU cc_start: 0.9394 (mp) cc_final: 0.9156 (mp) REVERT: C 173 MET cc_start: 0.9843 (mmm) cc_final: 0.9559 (mmm) REVERT: C 274 TRP cc_start: 0.8736 (t-100) cc_final: 0.8512 (t-100) REVERT: C 326 MET cc_start: 0.9221 (mmm) cc_final: 0.9008 (mmt) REVERT: D 33 MET cc_start: 0.9668 (mmm) cc_final: 0.9323 (mmm) REVERT: E 103 TYR cc_start: 0.9451 (t80) cc_final: 0.9218 (t80) REVERT: E 169 TYR cc_start: 0.7524 (m-10) cc_final: 0.7320 (m-10) REVERT: E 211 MET cc_start: 0.8420 (mmp) cc_final: 0.8184 (mmp) REVERT: F 199 GLU cc_start: 0.9443 (tp30) cc_final: 0.9240 (pt0) REVERT: J 1 MET cc_start: 0.7258 (tpp) cc_final: 0.6703 (tpp) outliers start: 1 outliers final: 1 residues processed: 163 average time/residue: 0.8982 time to fit residues: 244.5297 Evaluate side-chains 146 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 20.0000 chunk 119 optimal weight: 0.8980 chunk 320 optimal weight: 10.0000 chunk 262 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 385 optimal weight: 2.9990 chunk 416 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 chunk 382 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 131 GLN B 151 ASN B 560 ASN ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36843 Z= 0.215 Angle : 0.512 9.274 50130 Z= 0.297 Chirality : 0.035 0.360 5530 Planarity : 0.004 0.055 6291 Dihedral : 14.986 87.549 5930 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.13), residues: 4164 helix: 1.81 (0.10), residues: 2744 sheet: -0.59 (0.30), residues: 273 loop : -0.84 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 15 HIS 0.009 0.001 HIS J 86 PHE 0.019 0.001 PHE F 170 TYR 0.025 0.001 TYR B 174 ARG 0.011 0.000 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.9356 (mpp) cc_final: 0.8849 (mtp) REVERT: A 1149 MET cc_start: 0.8740 (ptp) cc_final: 0.8280 (ptp) REVERT: A 1375 MET cc_start: 0.8883 (mmm) cc_final: 0.8608 (mmm) REVERT: B 122 MET cc_start: 0.8014 (ttp) cc_final: 0.7537 (ptm) REVERT: B 205 LEU cc_start: 0.9589 (tp) cc_final: 0.9320 (tt) REVERT: B 1215 MET cc_start: 0.9318 (mtp) cc_final: 0.9050 (mtp) REVERT: B 1403 LEU cc_start: 0.9378 (mp) cc_final: 0.9083 (mp) REVERT: C 173 MET cc_start: 0.9831 (mmm) cc_final: 0.9501 (mmm) REVERT: C 326 MET cc_start: 0.9200 (mmm) cc_final: 0.8974 (mmt) REVERT: D 33 MET cc_start: 0.9653 (mmm) cc_final: 0.9387 (mmm) REVERT: D 51 GLU cc_start: 0.9266 (mp0) cc_final: 0.9064 (mp0) REVERT: E 93 MET cc_start: 0.9161 (mmt) cc_final: 0.8612 (mmm) REVERT: E 103 TYR cc_start: 0.9478 (t80) cc_final: 0.9240 (t80) REVERT: E 169 TYR cc_start: 0.7518 (m-10) cc_final: 0.7262 (m-10) REVERT: E 211 MET cc_start: 0.8366 (mmp) cc_final: 0.8122 (mmp) REVERT: G 18 LYS cc_start: 0.8958 (mmpt) cc_final: 0.8755 (mmmt) REVERT: J 1 MET cc_start: 0.7215 (tpp) cc_final: 0.6790 (tpp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.9294 time to fit residues: 251.3229 Evaluate side-chains 148 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 5.9990 chunk 290 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 387 optimal weight: 0.8980 chunk 409 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 366 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1407 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN ** B 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 ASN ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1192 GLN ** B1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN E 5 HIS ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 36843 Z= 0.378 Angle : 0.637 9.491 50130 Z= 0.374 Chirality : 0.038 0.353 5530 Planarity : 0.005 0.062 6291 Dihedral : 14.983 89.363 5930 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.13), residues: 4164 helix: 1.00 (0.10), residues: 2725 sheet: -1.01 (0.29), residues: 272 loop : -1.15 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 495 HIS 0.009 0.002 HIS B 59 PHE 0.024 0.002 PHE A 542 TYR 0.024 0.002 TYR A 174 ARG 0.011 0.001 ARG I 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 4.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9213 (mtp) cc_final: 0.9005 (mtp) REVERT: A 583 MET cc_start: 0.9348 (mpp) cc_final: 0.8813 (mtp) REVERT: A 1034 MET cc_start: 0.8689 (tpt) cc_final: 0.8436 (tpt) REVERT: A 1375 MET cc_start: 0.8983 (mmm) cc_final: 0.8773 (mmm) REVERT: B 122 MET cc_start: 0.8054 (ttp) cc_final: 0.7606 (ptm) REVERT: B 205 LEU cc_start: 0.9595 (tp) cc_final: 0.9334 (tt) REVERT: B 344 MET cc_start: 0.8097 (mmp) cc_final: 0.7365 (mmm) REVERT: B 632 MET cc_start: 0.9139 (mmp) cc_final: 0.8936 (mmm) REVERT: B 1215 MET cc_start: 0.9451 (mtp) cc_final: 0.9022 (mtp) REVERT: B 1403 LEU cc_start: 0.9427 (mp) cc_final: 0.9217 (mp) REVERT: C 173 MET cc_start: 0.9829 (mmm) cc_final: 0.9512 (mmm) REVERT: C 196 ASP cc_start: 0.8953 (m-30) cc_final: 0.8710 (m-30) REVERT: C 326 MET cc_start: 0.9186 (mmm) cc_final: 0.8959 (mmt) REVERT: D 33 MET cc_start: 0.9626 (mmm) cc_final: 0.9256 (mmm) REVERT: E 93 MET cc_start: 0.9231 (mmt) cc_final: 0.8875 (mmm) REVERT: E 103 TYR cc_start: 0.9503 (t80) cc_final: 0.9270 (t80) REVERT: E 211 MET cc_start: 0.8370 (mmp) cc_final: 0.8098 (mmp) REVERT: F 204 MET cc_start: 0.8234 (mmp) cc_final: 0.7779 (ttp) REVERT: G 18 LYS cc_start: 0.9119 (mmpt) cc_final: 0.8904 (mmmt) REVERT: J 1 MET cc_start: 0.7442 (tpp) cc_final: 0.7035 (tpp) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.9316 time to fit residues: 239.0465 Evaluate side-chains 145 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 20.0000 chunk 232 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 349 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 GLN ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36843 Z= 0.235 Angle : 0.525 9.300 50130 Z= 0.309 Chirality : 0.036 0.359 5530 Planarity : 0.004 0.060 6291 Dihedral : 14.911 86.799 5930 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.13), residues: 4164 helix: 1.42 (0.10), residues: 2735 sheet: -0.98 (0.29), residues: 273 loop : -1.02 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 495 HIS 0.006 0.001 HIS B 330 PHE 0.022 0.002 PHE A 542 TYR 0.026 0.001 TYR B 174 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.9320 (mpp) cc_final: 0.8793 (mtp) REVERT: A 674 MET cc_start: 0.2222 (mmm) cc_final: 0.1953 (mmm) REVERT: A 1034 MET cc_start: 0.8626 (tpt) cc_final: 0.8396 (tpt) REVERT: A 1375 MET cc_start: 0.8954 (mmm) cc_final: 0.8696 (mmm) REVERT: B 122 MET cc_start: 0.7974 (ttp) cc_final: 0.7534 (ptm) REVERT: B 205 LEU cc_start: 0.9615 (tp) cc_final: 0.9337 (tt) REVERT: B 344 MET cc_start: 0.8046 (mmp) cc_final: 0.7282 (mmm) REVERT: B 1215 MET cc_start: 0.9344 (mtp) cc_final: 0.8936 (mtp) REVERT: B 1403 LEU cc_start: 0.9426 (mp) cc_final: 0.9150 (mp) REVERT: C 173 MET cc_start: 0.9813 (mmm) cc_final: 0.9472 (mmm) REVERT: C 326 MET cc_start: 0.9169 (mmm) cc_final: 0.8928 (mmt) REVERT: D 33 MET cc_start: 0.9614 (mmm) cc_final: 0.9257 (mmm) REVERT: E 93 MET cc_start: 0.9175 (mmt) cc_final: 0.8828 (mmm) REVERT: E 103 TYR cc_start: 0.9519 (t80) cc_final: 0.9282 (t80) REVERT: E 211 MET cc_start: 0.8455 (mmp) cc_final: 0.8210 (mmp) REVERT: G 18 LYS cc_start: 0.9135 (mmpt) cc_final: 0.8919 (mmmt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.9584 time to fit residues: 245.3384 Evaluate side-chains 148 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 410 optimal weight: 4.9990 chunk 340 optimal weight: 10.0000 chunk 189 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 GLN ** B1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36843 Z= 0.283 Angle : 0.548 9.254 50130 Z= 0.324 Chirality : 0.036 0.356 5530 Planarity : 0.004 0.047 6291 Dihedral : 14.863 86.694 5930 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.13), residues: 4164 helix: 1.35 (0.10), residues: 2735 sheet: -1.08 (0.29), residues: 273 loop : -1.15 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 495 HIS 0.006 0.001 HIS B 330 PHE 0.025 0.002 PHE B 232 TYR 0.019 0.001 TYR A 174 ARG 0.004 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 4.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.9445 (mpp) cc_final: 0.8964 (mtp) REVERT: A 1034 MET cc_start: 0.8595 (tpt) cc_final: 0.8360 (tpt) REVERT: A 1149 MET cc_start: 0.8907 (ptp) cc_final: 0.8545 (ptp) REVERT: A 1375 MET cc_start: 0.8971 (mmm) cc_final: 0.8738 (mmm) REVERT: B 122 MET cc_start: 0.7963 (ttp) cc_final: 0.7516 (ptm) REVERT: B 205 LEU cc_start: 0.9611 (tp) cc_final: 0.9347 (tt) REVERT: B 344 MET cc_start: 0.8092 (mmp) cc_final: 0.7327 (mmm) REVERT: B 1215 MET cc_start: 0.9349 (mtp) cc_final: 0.8941 (mtp) REVERT: B 1403 LEU cc_start: 0.9397 (mp) cc_final: 0.9117 (mp) REVERT: C 173 MET cc_start: 0.9810 (mmm) cc_final: 0.9474 (mmm) REVERT: D 33 MET cc_start: 0.9588 (mmm) cc_final: 0.9213 (mmm) REVERT: E 93 MET cc_start: 0.9203 (mmt) cc_final: 0.8564 (mmm) REVERT: E 103 TYR cc_start: 0.9534 (t80) cc_final: 0.9303 (t80) REVERT: E 211 MET cc_start: 0.8462 (mmp) cc_final: 0.8221 (mmp) REVERT: J 1 MET cc_start: 0.7457 (tpp) cc_final: 0.7145 (tpp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.9592 time to fit residues: 239.8132 Evaluate side-chains 144 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 408 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1253 ASN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 36843 Z= 0.356 Angle : 0.619 10.288 50130 Z= 0.365 Chirality : 0.038 0.351 5530 Planarity : 0.005 0.051 6291 Dihedral : 14.892 87.430 5930 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.48 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4164 helix: 0.97 (0.10), residues: 2721 sheet: -1.24 (0.29), residues: 272 loop : -1.37 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 495 HIS 0.008 0.002 HIS B 330 PHE 0.026 0.002 PHE A 542 TYR 0.021 0.002 TYR A 174 ARG 0.008 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.9460 (mpp) cc_final: 0.8954 (mtp) REVERT: A 1034 MET cc_start: 0.8622 (tpt) cc_final: 0.8390 (tpt) REVERT: A 1149 MET cc_start: 0.8986 (ptp) cc_final: 0.8629 (ptp) REVERT: A 1375 MET cc_start: 0.8970 (mmm) cc_final: 0.8693 (mmm) REVERT: B 122 MET cc_start: 0.7784 (ttp) cc_final: 0.7468 (ptm) REVERT: B 205 LEU cc_start: 0.9621 (tp) cc_final: 0.9374 (tt) REVERT: B 1403 LEU cc_start: 0.9369 (mp) cc_final: 0.9069 (mp) REVERT: D 33 MET cc_start: 0.9576 (mmm) cc_final: 0.9223 (mmm) REVERT: D 47 MET cc_start: 0.8354 (tpp) cc_final: 0.8060 (tpp) REVERT: E 93 MET cc_start: 0.9263 (mmt) cc_final: 0.8540 (mmm) REVERT: E 211 MET cc_start: 0.8474 (mmp) cc_final: 0.8228 (mmp) REVERT: G 18 LYS cc_start: 0.9173 (mmpt) cc_final: 0.8935 (mmmt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.9911 time to fit residues: 242.6245 Evaluate side-chains 140 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 259 optimal weight: 0.0040 chunk 278 optimal weight: 0.3980 chunk 202 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 overall best weight: 2.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN ** B 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36843 Z= 0.187 Angle : 0.515 8.973 50130 Z= 0.298 Chirality : 0.035 0.358 5530 Planarity : 0.004 0.060 6291 Dihedral : 14.801 89.576 5930 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.03 % Allowed : 0.85 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.13), residues: 4164 helix: 1.56 (0.10), residues: 2726 sheet: -1.09 (0.29), residues: 273 loop : -1.12 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 274 HIS 0.012 0.001 HIS E 35 PHE 0.055 0.002 PHE B 855 TYR 0.022 0.001 TYR A 174 ARG 0.004 0.001 ARG B 709 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 4.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.9422 (mpp) cc_final: 0.8894 (mtp) REVERT: A 1042 MET cc_start: 0.8410 (mmt) cc_final: 0.7764 (mmm) REVERT: A 1149 MET cc_start: 0.8744 (ptp) cc_final: 0.8347 (ptp) REVERT: A 1375 MET cc_start: 0.8888 (mmm) cc_final: 0.8592 (mmm) REVERT: B 122 MET cc_start: 0.7670 (ttp) cc_final: 0.7343 (ptm) REVERT: B 205 LEU cc_start: 0.9635 (tp) cc_final: 0.9402 (tt) REVERT: B 925 MET cc_start: 0.8057 (ppp) cc_final: 0.7715 (ppp) REVERT: B 1215 MET cc_start: 0.9347 (mtp) cc_final: 0.8959 (mtp) REVERT: C 173 MET cc_start: 0.9794 (mmm) cc_final: 0.9456 (mmm) REVERT: D 33 MET cc_start: 0.9582 (mmm) cc_final: 0.9220 (mmm) REVERT: D 47 MET cc_start: 0.8602 (tpp) cc_final: 0.7973 (tpp) REVERT: E 93 MET cc_start: 0.9164 (mmt) cc_final: 0.8299 (mmm) REVERT: E 94 MET cc_start: 0.9597 (mmt) cc_final: 0.9308 (mmm) REVERT: E 204 MET cc_start: 0.9306 (mtm) cc_final: 0.8687 (mmp) REVERT: E 211 MET cc_start: 0.8393 (mmp) cc_final: 0.8154 (mmp) REVERT: F 204 MET cc_start: 0.8110 (mmp) cc_final: 0.7630 (ttp) REVERT: G 18 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8767 (mmmt) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.9641 time to fit residues: 243.2188 Evaluate side-chains 145 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 9.9990 chunk 391 optimal weight: 4.9990 chunk 357 optimal weight: 9.9990 chunk 380 optimal weight: 9.9990 chunk 229 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 344 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 379 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36843 Z= 0.246 Angle : 0.535 9.335 50130 Z= 0.312 Chirality : 0.036 0.353 5530 Planarity : 0.004 0.039 6291 Dihedral : 14.748 85.273 5930 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.13), residues: 4164 helix: 1.51 (0.10), residues: 2722 sheet: -1.09 (0.30), residues: 273 loop : -1.17 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 495 HIS 0.008 0.001 HIS B 936 PHE 0.031 0.002 PHE B 855 TYR 0.034 0.001 TYR B 550 ARG 0.034 0.000 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 4.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.9429 (mpp) cc_final: 0.8912 (mtp) REVERT: A 1042 MET cc_start: 0.8439 (mmt) cc_final: 0.7795 (mmm) REVERT: A 1149 MET cc_start: 0.8747 (ptp) cc_final: 0.8461 (ptp) REVERT: A 1375 MET cc_start: 0.8917 (mmm) cc_final: 0.8633 (mmm) REVERT: B 122 MET cc_start: 0.7709 (ttp) cc_final: 0.7399 (ptm) REVERT: B 205 LEU cc_start: 0.9649 (tp) cc_final: 0.9393 (tt) REVERT: B 925 MET cc_start: 0.8049 (ppp) cc_final: 0.7704 (ppp) REVERT: B 1034 MET cc_start: 0.8330 (mtp) cc_final: 0.7690 (mtp) REVERT: B 1215 MET cc_start: 0.9386 (mtp) cc_final: 0.8990 (mtp) REVERT: C 173 MET cc_start: 0.9799 (mmm) cc_final: 0.9472 (mmm) REVERT: D 33 MET cc_start: 0.9579 (mmm) cc_final: 0.9220 (mmm) REVERT: D 47 MET cc_start: 0.8645 (tpp) cc_final: 0.8081 (tpp) REVERT: E 93 MET cc_start: 0.9198 (mmt) cc_final: 0.8317 (mmm) REVERT: E 94 MET cc_start: 0.9612 (mmt) cc_final: 0.9309 (mmm) REVERT: E 204 MET cc_start: 0.9323 (mtm) cc_final: 0.8654 (mmp) REVERT: E 211 MET cc_start: 0.8395 (mmp) cc_final: 0.8145 (mmp) REVERT: F 204 MET cc_start: 0.8108 (mmp) cc_final: 0.7627 (ttp) REVERT: G 18 LYS cc_start: 0.9052 (mmpt) cc_final: 0.8816 (mmmt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.9619 time to fit residues: 237.6559 Evaluate side-chains 143 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 10.0000 chunk 402 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 422 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 336 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36843 Z= 0.268 Angle : 0.552 9.362 50130 Z= 0.323 Chirality : 0.036 0.351 5530 Planarity : 0.004 0.042 6291 Dihedral : 14.734 80.727 5930 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.13), residues: 4164 helix: 1.40 (0.10), residues: 2719 sheet: -1.20 (0.30), residues: 272 loop : -1.21 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 274 HIS 0.006 0.001 HIS A 825 PHE 0.026 0.002 PHE B 855 TYR 0.019 0.001 TYR A 174 ARG 0.017 0.001 ARG A1305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.9415 (mpp) cc_final: 0.8848 (mtp) REVERT: A 1042 MET cc_start: 0.8474 (mmt) cc_final: 0.7826 (mmm) REVERT: A 1149 MET cc_start: 0.8742 (ptp) cc_final: 0.8458 (ptp) REVERT: B 122 MET cc_start: 0.7721 (ttp) cc_final: 0.7412 (ptm) REVERT: B 205 LEU cc_start: 0.9628 (tp) cc_final: 0.9396 (tt) REVERT: B 1034 MET cc_start: 0.8346 (mtp) cc_final: 0.7729 (mtp) REVERT: B 1215 MET cc_start: 0.9377 (mtp) cc_final: 0.9016 (mtp) REVERT: B 1403 LEU cc_start: 0.9396 (mp) cc_final: 0.9156 (mm) REVERT: C 173 MET cc_start: 0.9791 (mmm) cc_final: 0.9461 (mmm) REVERT: D 33 MET cc_start: 0.9570 (mmm) cc_final: 0.9183 (mmm) REVERT: D 47 MET cc_start: 0.8647 (tpp) cc_final: 0.8075 (tpp) REVERT: D 81 MET cc_start: 0.9747 (mmp) cc_final: 0.9478 (mmp) REVERT: E 211 MET cc_start: 0.8421 (mmp) cc_final: 0.8173 (mmp) REVERT: G 18 LYS cc_start: 0.9113 (mmpt) cc_final: 0.8889 (mmmt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.9718 time to fit residues: 240.0729 Evaluate side-chains 142 residues out of total 3638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 310 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 336 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 345 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.023893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.016912 restraints weight = 1881284.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.017645 restraints weight = 976727.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.018122 restraints weight = 647969.019| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36843 Z= 0.191 Angle : 0.510 9.315 50130 Z= 0.295 Chirality : 0.035 0.354 5530 Planarity : 0.004 0.041 6291 Dihedral : 14.695 85.038 5930 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 4164 helix: 1.69 (0.10), residues: 2725 sheet: -1.08 (0.30), residues: 273 loop : -1.08 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 495 HIS 0.006 0.001 HIS A 825 PHE 0.025 0.001 PHE B 855 TYR 0.021 0.001 TYR A 174 ARG 0.007 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8328.92 seconds wall clock time: 147 minutes 42.11 seconds (8862.11 seconds total)