Starting phenix.real_space_refine on Thu Dec 26 04:23:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3g_15827/12_2024/8b3g_15827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3g_15827/12_2024/8b3g_15827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b3g_15827/12_2024/8b3g_15827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3g_15827/12_2024/8b3g_15827.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3g_15827/12_2024/8b3g_15827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3g_15827/12_2024/8b3g_15827.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 S 122 5.16 5 C 13572 2.51 5 N 3697 2.21 5 O 4018 1.98 5 H 21416 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42828 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2290 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1237 Classifications: {'peptide': 76} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "R" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1284 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Chain: "U" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1207 Classifications: {'peptide': 76} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 5627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5627 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 355} Chain: "c" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2451 Classifications: {'peptide': 148} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 140} Chain: "d" Number of atoms: 17196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 17196 Classifications: {'peptide': 1096} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1055} Chain breaks: 6 Chain: "e" Number of atoms: 11533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 11533 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 679} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3935 SG CYS R 42 71.630 64.426 44.129 1.00520.46 S ATOM 3974 SG CYS R 45 73.593 65.299 46.143 1.00574.49 S ATOM 4437 SG CYS R 83 74.428 61.747 45.892 1.00585.86 S ATOM 4312 SG CYS R 75 62.376 58.278 35.047 1.00501.27 S ATOM 4637 SG CYS R 94 63.873 58.560 39.155 1.00542.22 S ATOM 4106 SG CYS R 53 77.711 62.359 46.631 1.00616.98 S ATOM 4150 SG CYS R 56 81.627 62.009 45.539 1.00599.97 S ATOM 4215 SG CYS R 68 79.879 63.166 43.102 1.00575.23 S Time building chain proxies: 19.30, per 1000 atoms: 0.45 Number of scatterers: 42828 At special positions: 0 Unit cell: (110.7, 150.06, 186.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 122 16.00 O 4018 8.00 N 3697 7.00 C 13572 6.00 H 21416 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.41 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 6 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5046 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 44 sheets defined 31.8% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.660A pdb=" N ILE D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 98 through 110 removed outlier: 3.515A pdb=" N LEU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 removed outlier: 3.840A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 146 removed outlier: 3.612A pdb=" N TYR D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 35 removed outlier: 3.522A pdb=" N ILE N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'R' and resid 53 through 58 removed outlier: 4.205A pdb=" N ALA R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.049A pdb=" N ARG R 86 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 35 Processing helix chain 'U' and resid 55 through 60 removed outlier: 3.528A pdb=" N ASN U 60 " --> pdb=" O SER U 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 10 Processing helix chain 'a' and resid 14 through 29 removed outlier: 3.918A pdb=" N LEU a 18 " --> pdb=" O ASP a 14 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 15 removed outlier: 3.503A pdb=" N SER c 15 " --> pdb=" O GLU c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 35 removed outlier: 4.245A pdb=" N SER c 35 " --> pdb=" O ILE c 31 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 52 removed outlier: 3.736A pdb=" N GLN c 52 " --> pdb=" O ALA c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 72 Processing helix chain 'c' and resid 73 through 81 Processing helix chain 'c' and resid 82 through 91 Processing helix chain 'c' and resid 102 through 125 Processing helix chain 'c' and resid 128 through 141 Processing helix chain 'd' and resid 251 through 255 Processing helix chain 'd' and resid 366 through 370 removed outlier: 4.122A pdb=" N GLN d 370 " --> pdb=" O LEU d 367 " (cutoff:3.500A) Processing helix chain 'd' and resid 755 through 759 Processing helix chain 'd' and resid 986 through 990 Processing helix chain 'd' and resid 1044 through 1062 Processing helix chain 'd' and resid 1069 through 1074 Processing helix chain 'd' and resid 1091 through 1096 Processing helix chain 'd' and resid 1101 through 1109 Processing helix chain 'd' and resid 1125 through 1138 Processing helix chain 'e' and resid 57 through 75 Processing helix chain 'e' and resid 82 through 96 Processing helix chain 'e' and resid 98 through 122 removed outlier: 3.506A pdb=" N ALA e 109 " --> pdb=" O GLN e 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN e 115 " --> pdb=" O GLU e 111 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA e 116 " --> pdb=" O ASP e 112 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU e 119 " --> pdb=" O GLN e 115 " (cutoff:3.500A) Proline residue: e 120 - end of helix Processing helix chain 'e' and resid 127 through 153 removed outlier: 3.585A pdb=" N LYS e 133 " --> pdb=" O VAL e 129 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS e 142 " --> pdb=" O CYS e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 153 through 159 Processing helix chain 'e' and resid 159 through 164 removed outlier: 3.947A pdb=" N GLN e 163 " --> pdb=" O THR e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 182 Processing helix chain 'e' and resid 185 through 205 Processing helix chain 'e' and resid 210 through 224 Processing helix chain 'e' and resid 226 through 252 removed outlier: 3.580A pdb=" N GLU e 232 " --> pdb=" O LYS e 228 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU e 233 " --> pdb=" O ASP e 229 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS e 234 " --> pdb=" O SER e 230 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN e 252 " --> pdb=" O GLN e 248 " (cutoff:3.500A) Processing helix chain 'e' and resid 255 through 277 removed outlier: 3.648A pdb=" N ASN e 261 " --> pdb=" O PRO e 257 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE e 275 " --> pdb=" O GLY e 271 " (cutoff:3.500A) Processing helix chain 'e' and resid 279 through 281 No H-bonds generated for 'chain 'e' and resid 279 through 281' Processing helix chain 'e' and resid 282 through 295 Processing helix chain 'e' and resid 298 through 314 removed outlier: 4.670A pdb=" N ASP e 308 " --> pdb=" O GLN e 304 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS e 309 " --> pdb=" O LYS e 305 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP e 312 " --> pdb=" O ASP e 308 " (cutoff:3.500A) Processing helix chain 'e' and resid 315 through 327 Processing helix chain 'e' and resid 331 through 353 removed outlier: 3.600A pdb=" N HIS e 339 " --> pdb=" O ALA e 335 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR e 349 " --> pdb=" O LYS e 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA e 350 " --> pdb=" O THR e 346 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE e 351 " --> pdb=" O PHE e 347 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL e 352 " --> pdb=" O GLY e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 354 through 358 Processing helix chain 'e' and resid 361 through 379 Processing helix chain 'e' and resid 383 through 399 removed outlier: 3.883A pdb=" N ASN e 399 " --> pdb=" O GLU e 395 " (cutoff:3.500A) Processing helix chain 'e' and resid 403 through 418 removed outlier: 3.629A pdb=" N GLU e 407 " --> pdb=" O ASN e 403 " (cutoff:3.500A) Processing helix chain 'e' and resid 425 through 441 removed outlier: 3.605A pdb=" N ARG e 431 " --> pdb=" O GLU e 427 " (cutoff:3.500A) Processing helix chain 'e' and resid 445 through 463 removed outlier: 3.537A pdb=" N PHE e 449 " --> pdb=" O GLY e 445 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA e 451 " --> pdb=" O ASP e 447 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 488 removed outlier: 7.632A pdb=" N ALA e 485 " --> pdb=" O HIS e 481 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ALA e 486 " --> pdb=" O GLU e 482 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE e 487 " --> pdb=" O CYS e 483 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR e 488 " --> pdb=" O GLY e 484 " (cutoff:3.500A) Processing helix chain 'e' and resid 488 through 515 removed outlier: 3.577A pdb=" N MET e 494 " --> pdb=" O LYS e 490 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE e 495 " --> pdb=" O LEU e 491 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP e 503 " --> pdb=" O GLU e 499 " (cutoff:3.500A) Processing helix chain 'e' and resid 544 through 562 removed outlier: 3.675A pdb=" N LYS e 549 " --> pdb=" O PRO e 545 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU e 550 " --> pdb=" O GLU e 546 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN e 551 " --> pdb=" O MET e 547 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU e 552 " --> pdb=" O ILE e 548 " (cutoff:3.500A) Processing helix chain 'e' and resid 593 through 600 Processing helix chain 'e' and resid 610 through 618 removed outlier: 3.793A pdb=" N ALA e 616 " --> pdb=" O GLU e 612 " (cutoff:3.500A) Processing helix chain 'e' and resid 620 through 633 Processing helix chain 'e' and resid 693 through 708 Processing helix chain 'e' and resid 712 through 723 removed outlier: 3.581A pdb=" N LEU e 719 " --> pdb=" O LEU e 715 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR e 720 " --> pdb=" O VAL e 716 " (cutoff:3.500A) Processing helix chain 'e' and resid 728 through 742 Processing sheet with id=AA1, first strand: chain 'D' and resid 21 through 25 Processing sheet with id=AA2, first strand: chain 'N' and resid 12 through 16 removed outlier: 7.825A pdb=" N LEU N 67 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU N 69 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL N 70 " --> pdb=" O ARG N 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 522 through 529 removed outlier: 3.813A pdb=" N VAL e 577 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL R 30 " --> pdb=" O LEU e 573 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU e 573 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N LEU R 32 " --> pdb=" O THR e 571 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR e 571 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 10.645A pdb=" N ALA R 34 " --> pdb=" O TRP e 569 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N TRP e 569 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY e 585 " --> pdb=" O PHE e 582 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE e 582 " --> pdb=" O GLY e 585 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 522 through 529 removed outlier: 3.813A pdb=" N VAL e 577 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL R 30 " --> pdb=" O LEU e 573 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU e 573 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N LEU R 32 " --> pdb=" O THR e 571 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR e 571 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 10.645A pdb=" N ALA R 34 " --> pdb=" O TRP e 569 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N TRP e 569 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE e 667 " --> pdb=" O LYS e 586 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU e 588 " --> pdb=" O ILE e 667 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'U' and resid 13 through 16 Processing sheet with id=AA7, first strand: chain 'a' and resid 30 through 32 removed outlier: 3.501A pdb=" N LEU a 359 " --> pdb=" O SER a 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 37 through 38 removed outlier: 7.387A pdb=" N ASP a 37 " --> pdb=" O CYS a 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.405A pdb=" N GLY a 62 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU a 49 " --> pdb=" O LEU a 60 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU a 60 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE a 51 " --> pdb=" O TYR a 58 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR a 58 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET a 59 " --> pdb=" O TYR a 71 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE a 68 " --> pdb=" O ILE a 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS a 88 " --> pdb=" O LEU a 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 102 through 107 removed outlier: 3.762A pdb=" N THR a 104 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL a 137 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL a 126 " --> pdb=" O ALA a 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 144 through 149 removed outlier: 3.707A pdb=" N SER a 146 " --> pdb=" O GLY a 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 191 through 194 removed outlier: 3.545A pdb=" N ILE a 224 " --> pdb=" O LEU a 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 248 through 253 removed outlier: 3.985A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 298 through 299 removed outlier: 3.560A pdb=" N THR a 298 " --> pdb=" O PHE a 309 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE a 316 " --> pdb=" O MET a 329 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET a 329 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL a 318 " --> pdb=" O ILE a 327 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 1007 through 1009 removed outlier: 3.510A pdb=" N PHE d1030 " --> pdb=" O GLY d1038 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE d1037 " --> pdb=" O ALA d 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 15 through 21 removed outlier: 3.890A pdb=" N GLY d 17 " --> pdb=" O ALA d 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 38 through 41 removed outlier: 4.033A pdb=" N LYS d 53 " --> pdb=" O ILE d 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 61 through 67 removed outlier: 6.620A pdb=" N LEU d 80 " --> pdb=" O ALA d 62 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET d 64 " --> pdb=" O PHE d 78 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE d 78 " --> pdb=" O MET d 64 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU d 66 " --> pdb=" O LEU d 76 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU d 76 " --> pdb=" O LEU d 66 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA d 104 " --> pdb=" O ILE d 88 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU d 90 " --> pdb=" O THR d 102 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR d 102 " --> pdb=" O GLU d 90 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS d 92 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE d 100 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER d 94 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE d 98 " --> pdb=" O SER d 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 121 through 124 removed outlier: 3.740A pdb=" N ILE d 121 " --> pdb=" O ARG d 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 164 through 169 removed outlier: 6.580A pdb=" N VAL d 181 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL d 167 " --> pdb=" O CYS d 179 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS d 179 " --> pdb=" O VAL d 167 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE d 169 " --> pdb=" O THR d 177 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR d 177 " --> pdb=" O PHE d 169 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 220 through 221 removed outlier: 3.572A pdb=" N ILE d 248 " --> pdb=" O ILE d 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 258 through 263 removed outlier: 3.579A pdb=" N LEU d 273 " --> pdb=" O PHE d 281 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU d 280 " --> pdb=" O LEU d 304 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU d 304 " --> pdb=" O LEU d 280 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N MET d 282 " --> pdb=" O VAL d 302 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL d 302 " --> pdb=" O MET d 282 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU d 284 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU d 300 " --> pdb=" O LEU d 284 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU d 286 " --> pdb=" O LYS d 298 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 313 through 318 removed outlier: 4.927A pdb=" N LEU d 314 " --> pdb=" O GLY d 325 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY d 325 " --> pdb=" O LEU d 314 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR d 316 " --> pdb=" O PHE d 323 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE d 323 " --> pdb=" O TYR d 316 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP d 318 " --> pdb=" O VAL d 321 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER d 331 " --> pdb=" O THR d 352 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR d 352 " --> pdb=" O SER d 331 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU d 333 " --> pdb=" O MET d 350 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 362 through 365 Processing sheet with id=AC7, first strand: chain 'd' and resid 386 through 387 Processing sheet with id=AC8, first strand: chain 'd' and resid 390 through 393 Processing sheet with id=AC9, first strand: chain 'd' and resid 396 through 403 removed outlier: 5.707A pdb=" N GLU d 398 " --> pdb=" O THR d 703 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR d 703 " --> pdb=" O GLU d 398 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 407 through 413 removed outlier: 4.444A pdb=" N VAL d 435 " --> pdb=" O THR d 446 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 470 through 471 removed outlier: 3.507A pdb=" N SER d 488 " --> pdb=" O LEU d 478 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER d 480 " --> pdb=" O LEU d 486 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU d 486 " --> pdb=" O SER d 480 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 500 through 503 removed outlier: 6.614A pdb=" N LEU d 516 " --> pdb=" O HIS d 531 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS d 531 " --> pdb=" O LEU d 516 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR d 518 " --> pdb=" O ILE d 529 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 538 through 542 removed outlier: 6.519A pdb=" N GLY d 559 " --> pdb=" O ALA d 539 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU d 541 " --> pdb=" O ALA d 557 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA d 557 " --> pdb=" O LEU d 541 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER d 565 " --> pdb=" O LEU d 560 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS d 578 " --> pdb=" O ILE d 568 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS d 570 " --> pdb=" O LEU d 576 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU d 576 " --> pdb=" O LYS d 570 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 588 through 596 removed outlier: 3.521A pdb=" N SER d 590 " --> pdb=" O ALA d 605 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE d 614 " --> pdb=" O LEU d 602 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA d 610 " --> pdb=" O LEU d 606 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU d 611 " --> pdb=" O LYS d 628 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS d 628 " --> pdb=" O LEU d 611 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR d 613 " --> pdb=" O ARG d 626 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG d 626 " --> pdb=" O TYR d 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 637 through 642 removed outlier: 8.466A pdb=" N THR d 647 " --> pdb=" O SER d 661 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER d 661 " --> pdb=" O THR d 647 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 681 through 682 Processing sheet with id=AD8, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.175A pdb=" N SER d 738 " --> pdb=" O PRO d 721 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS d 723 " --> pdb=" O LEU d 736 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS d 732 " --> pdb=" O GLN d 727 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER d 737 " --> pdb=" O ASN d 790 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG d 739 " --> pdb=" O VAL d 788 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS d 789 " --> pdb=" O GLN d 806 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN d 806 " --> pdb=" O HIS d 789 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU d 791 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA d 804 " --> pdb=" O LEU d 791 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE d 793 " --> pdb=" O LEU d 802 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER d 764 " --> pdb=" O GLN d 806 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.468A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL d 850 " --> pdb=" O VAL d 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.468A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY d 846 " --> pdb=" O VAL d 866 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 874 through 876 Processing sheet with id=AE3, first strand: chain 'd' and resid 890 through 893 removed outlier: 6.793A pdb=" N LEU d 890 " --> pdb=" O GLU d 902 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 911 through 917 removed outlier: 3.731A pdb=" N ASN d 941 " --> pdb=" O LYS d 936 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 954 through 961 removed outlier: 6.489A pdb=" N ASN d 964 " --> pdb=" O LEU d 960 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU d 974 " --> pdb=" O LEU d 997 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU d 997 " --> pdb=" O LEU d 974 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL d 976 " --> pdb=" O VAL d 995 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'd' and resid 1076 through 1078 Processing sheet with id=AE7, first strand: chain 'e' and resid 607 through 609 removed outlier: 3.502A pdb=" N PHE e 654 " --> pdb=" O PHE e 608 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 709 through 711 905 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.16 Time building geometry restraints manager: 14.39 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: 21370 1.03 - 1.23: 117 1.23 - 1.42: 8940 1.42 - 1.62: 12620 1.62 - 1.82: 187 Bond restraints: 43234 Sorted by residual: bond pdb=" ND2 ASN d 392 " pdb="HD21 ASN d 392 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN d 392 " pdb="HD22 ASN d 392 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CA ASN d 392 " pdb=" C ASN d 392 " ideal model delta sigma weight residual 1.524 1.453 0.071 1.31e-02 5.83e+03 2.95e+01 bond pdb=" C PRO c 98 " pdb=" N LEU c 99 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.07e-02 2.33e+03 1.96e+01 bond pdb=" CA GLN d 708 " pdb=" CB GLN d 708 " ideal model delta sigma weight residual 1.529 1.456 0.073 1.66e-02 3.63e+03 1.93e+01 ... (remaining 43229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 77393 2.07 - 4.14: 736 4.14 - 6.20: 90 6.20 - 8.27: 7 8.27 - 10.34: 3 Bond angle restraints: 78229 Sorted by residual: angle pdb=" N ILE d 394 " pdb=" CA ILE d 394 " pdb=" C ILE d 394 " ideal model delta sigma weight residual 106.32 96.62 9.70 1.61e+00 3.86e-01 3.63e+01 angle pdb=" CA PRO e 520 " pdb=" N PRO e 520 " pdb=" CD PRO e 520 " ideal model delta sigma weight residual 112.00 103.97 8.03 1.40e+00 5.10e-01 3.29e+01 angle pdb=" C ILE d 396 " pdb=" CA ILE d 396 " pdb=" CB ILE d 396 " ideal model delta sigma weight residual 111.81 104.34 7.47 1.37e+00 5.33e-01 2.98e+01 angle pdb=" N SER d 929 " pdb=" CA SER d 929 " pdb=" C SER d 929 " ideal model delta sigma weight residual 110.80 119.33 -8.53 2.13e+00 2.20e-01 1.60e+01 angle pdb=" CA PRO c 100 " pdb=" N PRO c 100 " pdb=" CD PRO c 100 " ideal model delta sigma weight residual 112.00 106.45 5.55 1.40e+00 5.10e-01 1.57e+01 ... (remaining 78224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 18021 17.59 - 35.19: 1695 35.19 - 52.78: 363 52.78 - 70.38: 94 70.38 - 87.97: 20 Dihedral angle restraints: 20193 sinusoidal: 11109 harmonic: 9084 Sorted by residual: dihedral pdb=" CA ILE d 884 " pdb=" C ILE d 884 " pdb=" N ASN d 885 " pdb=" CA ASN d 885 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ASN e 57 " pdb=" C ASN e 57 " pdb=" N TYR e 58 " pdb=" CA TYR e 58 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ARG e 51 " pdb=" C ARG e 51 " pdb=" N PRO e 52 " pdb=" CA PRO e 52 " ideal model delta harmonic sigma weight residual -180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 20190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2835 0.059 - 0.118: 432 0.118 - 0.178: 45 0.178 - 0.237: 2 0.237 - 0.296: 1 Chirality restraints: 3315 Sorted by residual: chirality pdb=" CB ILE d 396 " pdb=" CA ILE d 396 " pdb=" CG1 ILE d 396 " pdb=" CG2 ILE d 396 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ILE d 396 " pdb=" N ILE d 396 " pdb=" C ILE d 396 " pdb=" CB ILE d 396 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLN d 708 " pdb=" N GLN d 708 " pdb=" C GLN d 708 " pdb=" CB GLN d 708 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 3312 not shown) Planarity restraints: 6360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN d 708 " -0.065 2.00e-02 2.50e+03 6.62e-02 6.56e+01 pdb=" CD GLN d 708 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN d 708 " 0.055 2.00e-02 2.50e+03 pdb=" NE2 GLN d 708 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN d 708 " 0.096 2.00e-02 2.50e+03 pdb="HE22 GLN d 708 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 391 " -0.035 2.00e-02 2.50e+03 6.82e-02 4.66e+01 pdb=" C ARG d 391 " 0.118 2.00e-02 2.50e+03 pdb=" O ARG d 391 " -0.044 2.00e-02 2.50e+03 pdb=" N ASN d 392 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE d 396 " 0.028 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" N HIS d 397 " -0.093 2.00e-02 2.50e+03 pdb=" CA HIS d 397 " 0.022 2.00e-02 2.50e+03 pdb=" H HIS d 397 " 0.043 2.00e-02 2.50e+03 ... (remaining 6357 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.35: 20 1.35 - 2.16: 1670 2.16 - 2.98: 123528 2.98 - 3.79: 179859 3.79 - 4.60: 311414 Warning: very small nonbonded interaction distances. Nonbonded interactions: 616491 Sorted by model distance: nonbonded pdb="HG12 ILE d 394 " pdb=" OE1 GLN d 708 " model vdw 0.540 2.620 nonbonded pdb=" HE3 LYS a 335 " pdb=" HB3 ASN c 141 " model vdw 0.642 2.440 nonbonded pdb="HH22 ARG a 40 " pdb=" HD2 HIS c 136 " model vdw 0.644 1.680 nonbonded pdb="HH12 ARG a 40 " pdb=" CG HIS c 136 " model vdw 0.784 2.800 nonbonded pdb="HG23 ILE d 394 " pdb=" OD1 ASP d 705 " model vdw 0.856 2.620 ... (remaining 616486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.800 Extract box with map and model: 1.700 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 107.340 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.130 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 21818 Z= 0.352 Angle : 0.670 9.704 29470 Z= 0.367 Chirality : 0.044 0.296 3315 Planarity : 0.005 0.136 3787 Dihedral : 13.895 87.973 8192 Min Nonbonded Distance : 0.968 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.13 % Allowed : 0.17 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 2653 helix: 0.11 (0.19), residues: 759 sheet: -2.42 (0.19), residues: 667 loop : -1.62 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 272 HIS 0.009 0.001 HIS R 48 PHE 0.032 0.002 PHE e 48 TYR 0.018 0.002 TYR a 145 ARG 0.014 0.001 ARG c 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 3.797 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 MET cc_start: 0.6978 (mmt) cc_final: 0.6454 (mmp) REVERT: N 58 ASP cc_start: 0.9660 (m-30) cc_final: 0.9286 (m-30) REVERT: U 4 PHE cc_start: 0.9862 (m-80) cc_final: 0.9651 (m-10) REVERT: d 64 MET cc_start: 0.9168 (ttm) cc_final: 0.8805 (ptm) REVERT: d 437 MET cc_start: -0.2099 (tpp) cc_final: -0.2370 (tmm) REVERT: d 954 MET cc_start: 0.8616 (mmm) cc_final: 0.8322 (mmm) REVERT: d 962 ASP cc_start: 0.9722 (m-30) cc_final: 0.9494 (p0) REVERT: d 1099 ASP cc_start: 0.9541 (m-30) cc_final: 0.9283 (p0) REVERT: e 146 MET cc_start: 0.9370 (tpp) cc_final: 0.9024 (tpp) REVERT: e 251 MET cc_start: 0.9076 (tpp) cc_final: 0.8655 (mmm) REVERT: e 505 MET cc_start: 0.9592 (mmp) cc_final: 0.9334 (mmm) REVERT: e 539 MET cc_start: 0.7536 (ppp) cc_final: 0.5593 (ppp) outliers start: 3 outliers final: 2 residues processed: 169 average time/residue: 1.1612 time to fit residues: 277.4188 Evaluate side-chains 127 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 110 optimal weight: 0.0050 chunk 68 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN R 57 GLN R 59 ASN R 98 ASN a 228 GLN d 93 GLN ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 677 ASN d 708 GLN ** d 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 877 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 GLN e 164 ASN e 309 HIS e 338 GLN e 399 ASN ** e 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 21818 Z= 0.292 Angle : 0.626 7.874 29470 Z= 0.342 Chirality : 0.042 0.168 3315 Planarity : 0.005 0.098 3787 Dihedral : 5.238 75.728 2892 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.75 (0.16), residues: 2653 helix: 0.45 (0.18), residues: 790 sheet: -2.24 (0.19), residues: 676 loop : -1.51 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP e 63 HIS 0.011 0.001 HIS c 136 PHE 0.023 0.002 PHE c 137 TYR 0.013 0.002 TYR a 100 ARG 0.007 0.001 ARG a 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 3.657 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 MET cc_start: 0.7153 (mmt) cc_final: 0.6444 (mmp) REVERT: U 4 PHE cc_start: 0.9862 (m-80) cc_final: 0.9617 (m-10) REVERT: d 64 MET cc_start: 0.9158 (ttm) cc_final: 0.8946 (ttp) REVERT: d 437 MET cc_start: -0.1732 (tpp) cc_final: -0.1955 (tmm) REVERT: d 962 ASP cc_start: 0.9779 (m-30) cc_final: 0.9519 (p0) REVERT: d 1014 MET cc_start: 0.7910 (tmm) cc_final: 0.7613 (tmm) REVERT: e 146 MET cc_start: 0.9535 (tpp) cc_final: 0.9201 (tpp) REVERT: e 251 MET cc_start: 0.9205 (tpp) cc_final: 0.8612 (mmm) REVERT: e 322 MET cc_start: 0.9777 (ttm) cc_final: 0.9488 (tmm) REVERT: e 505 MET cc_start: 0.9572 (mmp) cc_final: 0.9276 (mmm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 1.1577 time to fit residues: 211.3742 Evaluate side-chains 111 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 132 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 7 HIS D 34 GLN a 183 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 852 GLN d1106 GLN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 163 GLN ** e 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 657 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 21818 Z= 0.372 Angle : 0.690 12.177 29470 Z= 0.376 Chirality : 0.041 0.157 3315 Planarity : 0.005 0.088 3787 Dihedral : 5.201 72.904 2892 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.95 (0.15), residues: 2653 helix: 0.25 (0.18), residues: 779 sheet: -2.28 (0.19), residues: 645 loop : -1.68 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP d 561 HIS 0.014 0.002 HIS c 136 PHE 0.024 0.002 PHE d 949 TYR 0.021 0.002 TYR a 100 ARG 0.008 0.001 ARG d 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 3.654 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: D 147 MET cc_start: 0.7626 (mmt) cc_final: 0.6976 (mmp) REVERT: U 4 PHE cc_start: 0.9818 (m-80) cc_final: 0.9561 (m-10) REVERT: d 57 MET cc_start: 0.8503 (tpt) cc_final: 0.8261 (tpp) REVERT: d 437 MET cc_start: -0.0018 (tpp) cc_final: -0.0322 (tmm) REVERT: d 910 MET cc_start: 0.8713 (mmt) cc_final: 0.8460 (mmt) REVERT: d 954 MET cc_start: 0.9318 (mmm) cc_final: 0.8745 (mmm) REVERT: d 962 ASP cc_start: 0.9781 (m-30) cc_final: 0.9507 (p0) REVERT: d 1014 MET cc_start: 0.8422 (tmm) cc_final: 0.8132 (tmm) REVERT: e 146 MET cc_start: 0.9572 (tpp) cc_final: 0.9210 (tpp) REVERT: e 251 MET cc_start: 0.9213 (tpp) cc_final: 0.8649 (mmm) REVERT: e 322 MET cc_start: 0.9787 (ttm) cc_final: 0.9480 (tmm) REVERT: e 475 MET cc_start: 0.9821 (tpp) cc_final: 0.9601 (tpp) REVERT: e 505 MET cc_start: 0.9382 (mmp) cc_final: 0.9120 (mmm) REVERT: e 547 MET cc_start: 0.9089 (mmm) cc_final: 0.8093 (tpp) REVERT: e 704 MET cc_start: 0.8747 (ttp) cc_final: 0.8237 (tpp) outliers start: 2 outliers final: 1 residues processed: 118 average time/residue: 1.1549 time to fit residues: 191.0422 Evaluate side-chains 101 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 236 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 156 ASN ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 511 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21818 Z= 0.250 Angle : 0.574 7.128 29470 Z= 0.312 Chirality : 0.041 0.152 3315 Planarity : 0.004 0.100 3787 Dihedral : 5.142 70.668 2892 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.66 (0.16), residues: 2653 helix: 0.71 (0.18), residues: 768 sheet: -2.21 (0.19), residues: 620 loop : -1.61 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP d1073 HIS 0.012 0.002 HIS d 536 PHE 0.027 0.002 PHE D 62 TYR 0.014 0.002 TYR d 718 ARG 0.005 0.000 ARG c 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 3.796 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: D 147 MET cc_start: 0.7569 (mmt) cc_final: 0.6920 (mmp) REVERT: U 4 PHE cc_start: 0.9856 (m-80) cc_final: 0.9647 (m-10) REVERT: d 835 MET cc_start: 0.6386 (mmm) cc_final: 0.5587 (mmm) REVERT: d 910 MET cc_start: 0.8684 (mmt) cc_final: 0.8388 (mmt) REVERT: d 962 ASP cc_start: 0.9739 (m-30) cc_final: 0.9510 (p0) REVERT: e 251 MET cc_start: 0.9230 (tpp) cc_final: 0.8634 (mmm) REVERT: e 322 MET cc_start: 0.9790 (ttm) cc_final: 0.9485 (tmm) REVERT: e 505 MET cc_start: 0.9335 (mmp) cc_final: 0.9086 (mmm) REVERT: e 547 MET cc_start: 0.9160 (mmm) cc_final: 0.8242 (tpp) REVERT: e 704 MET cc_start: 0.8816 (ttp) cc_final: 0.8284 (tpp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 1.0907 time to fit residues: 165.8236 Evaluate side-chains 96 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 211 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 HIS c 49 GLN ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 337 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 663 ASN ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 759 GLN d 877 ASN d 907 ASN d1049 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 163 GLN e 181 HIS ** e 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 363 GLN e 514 ASN e 603 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 21818 Z= 0.513 Angle : 0.826 10.044 29470 Z= 0.451 Chirality : 0.044 0.381 3315 Planarity : 0.006 0.067 3787 Dihedral : 5.683 69.897 2892 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.88 % Favored : 92.05 % Rotamer: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.15), residues: 2653 helix: -0.49 (0.17), residues: 779 sheet: -2.43 (0.19), residues: 617 loop : -1.94 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP e 533 HIS 0.011 0.003 HIS d 999 PHE 0.031 0.003 PHE d 650 TYR 0.029 0.003 TYR a 100 ARG 0.010 0.001 ARG c 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 3.823 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: D 147 MET cc_start: 0.6608 (mmt) cc_final: 0.5845 (mmp) REVERT: a 149 MET cc_start: 0.9017 (mtm) cc_final: 0.8650 (mtp) REVERT: d 910 MET cc_start: 0.8630 (mmt) cc_final: 0.8342 (mmt) REVERT: d 962 ASP cc_start: 0.9718 (m-30) cc_final: 0.9458 (p0) REVERT: d 1014 MET cc_start: 0.8619 (tmm) cc_final: 0.8408 (tmm) REVERT: e 146 MET cc_start: 0.9575 (tpp) cc_final: 0.9231 (tpp) REVERT: e 251 MET cc_start: 0.9235 (tpp) cc_final: 0.8663 (mmm) REVERT: e 322 MET cc_start: 0.9796 (ttm) cc_final: 0.9493 (tmm) REVERT: e 505 MET cc_start: 0.9218 (mmp) cc_final: 0.8956 (mmm) REVERT: e 704 MET cc_start: 0.8804 (ttp) cc_final: 0.8478 (tpp) outliers start: 2 outliers final: 2 residues processed: 98 average time/residue: 1.0520 time to fit residues: 149.5214 Evaluate side-chains 91 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 85 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN c 49 GLN ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d1056 ASN ** e 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 309 HIS ** e 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21818 Z= 0.328 Angle : 0.648 6.904 29470 Z= 0.359 Chirality : 0.042 0.153 3315 Planarity : 0.005 0.064 3787 Dihedral : 5.573 67.736 2892 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.15), residues: 2653 helix: -0.29 (0.17), residues: 779 sheet: -2.50 (0.19), residues: 631 loop : -1.94 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP e 533 HIS 0.018 0.002 HIS e 113 PHE 0.058 0.003 PHE D 69 TYR 0.019 0.002 TYR d 678 ARG 0.005 0.001 ARG c 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 3.626 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: D 72 ARG cc_start: 0.9778 (mtp-110) cc_final: 0.9393 (mmp80) REVERT: D 81 ASN cc_start: 0.8426 (m110) cc_final: 0.8186 (m110) REVERT: D 147 MET cc_start: 0.6717 (mmt) cc_final: 0.5933 (mmm) REVERT: a 59 MET cc_start: 0.9839 (ttt) cc_final: 0.9564 (tpp) REVERT: d 835 MET cc_start: 0.7780 (mmm) cc_final: 0.7377 (mmm) REVERT: d 962 ASP cc_start: 0.9709 (m-30) cc_final: 0.9430 (p0) REVERT: e 251 MET cc_start: 0.9128 (tpp) cc_final: 0.8606 (mmm) REVERT: e 322 MET cc_start: 0.9789 (ttm) cc_final: 0.9458 (tmm) REVERT: e 704 MET cc_start: 0.8847 (ttp) cc_final: 0.8503 (tpp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.9804 time to fit residues: 135.6829 Evaluate side-chains 88 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 245 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 overall best weight: 6.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN R 98 ASN ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 990 GLN ** e 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 339 HIS ** e 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 722 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21818 Z= 0.321 Angle : 0.625 6.929 29470 Z= 0.345 Chirality : 0.041 0.166 3315 Planarity : 0.005 0.058 3787 Dihedral : 5.540 69.514 2892 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2653 helix: -0.09 (0.17), residues: 781 sheet: -2.49 (0.19), residues: 638 loop : -1.91 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 139 HIS 0.008 0.002 HIS c 136 PHE 0.033 0.002 PHE e 178 TYR 0.020 0.002 TYR d 58 ARG 0.022 0.001 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 3.799 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: D 147 MET cc_start: 0.6823 (mmt) cc_final: 0.6042 (mmm) REVERT: a 59 MET cc_start: 0.9851 (ttt) cc_final: 0.9605 (tpp) REVERT: d 835 MET cc_start: 0.7907 (mmm) cc_final: 0.7536 (mmm) REVERT: d 910 MET cc_start: 0.8702 (mmt) cc_final: 0.8392 (mmt) REVERT: d 962 ASP cc_start: 0.9762 (m-30) cc_final: 0.9463 (p0) REVERT: d 1105 MET cc_start: 0.8899 (ttt) cc_final: 0.8642 (ttt) REVERT: e 322 MET cc_start: 0.9802 (ttm) cc_final: 0.9470 (tmm) REVERT: e 704 MET cc_start: 0.8814 (ttp) cc_final: 0.8306 (tpp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 1.0342 time to fit residues: 138.9367 Evaluate side-chains 86 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 156 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21818 Z= 0.223 Angle : 0.557 6.891 29470 Z= 0.305 Chirality : 0.041 0.149 3315 Planarity : 0.004 0.037 3787 Dihedral : 5.353 68.790 2892 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.16), residues: 2653 helix: 0.37 (0.18), residues: 784 sheet: -2.38 (0.19), residues: 639 loop : -1.82 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP e 63 HIS 0.008 0.001 HIS d 22 PHE 0.018 0.002 PHE D 69 TYR 0.016 0.002 TYR d 678 ARG 0.009 0.001 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.753 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: D 72 ARG cc_start: 0.9809 (mtp-110) cc_final: 0.9443 (mmp80) REVERT: D 81 ASN cc_start: 0.8560 (m110) cc_final: 0.8341 (m110) REVERT: D 147 MET cc_start: 0.6824 (mmt) cc_final: 0.6008 (mmm) REVERT: a 59 MET cc_start: 0.9846 (ttt) cc_final: 0.9596 (tpp) REVERT: d 962 ASP cc_start: 0.9769 (m-30) cc_final: 0.9488 (p0) REVERT: e 251 MET cc_start: 0.9091 (tpp) cc_final: 0.8482 (mmm) REVERT: e 322 MET cc_start: 0.9811 (ttm) cc_final: 0.9460 (tmm) REVERT: e 547 MET cc_start: 0.9196 (mmm) cc_final: 0.8314 (tpp) REVERT: e 704 MET cc_start: 0.8890 (ttp) cc_final: 0.8489 (tpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 1.0022 time to fit residues: 135.4930 Evaluate side-chains 87 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 242 optimal weight: 20.0000 chunk 221 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 337 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21818 Z= 0.295 Angle : 0.599 8.114 29470 Z= 0.328 Chirality : 0.041 0.148 3315 Planarity : 0.004 0.037 3787 Dihedral : 5.366 68.956 2892 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.16), residues: 2653 helix: 0.32 (0.18), residues: 788 sheet: -2.39 (0.19), residues: 671 loop : -1.81 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP e 533 HIS 0.007 0.002 HIS c 136 PHE 0.023 0.002 PHE e 495 TYR 0.015 0.002 TYR a 81 ARG 0.006 0.001 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.841 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: D 72 ARG cc_start: 0.9827 (mtp-110) cc_final: 0.9440 (mmp80) REVERT: D 81 ASN cc_start: 0.8373 (m110) cc_final: 0.8167 (m110) REVERT: D 147 MET cc_start: 0.6873 (mmt) cc_final: 0.6069 (mmm) REVERT: d 910 MET cc_start: 0.8709 (mmt) cc_final: 0.8385 (mmt) REVERT: d 962 ASP cc_start: 0.9748 (m-30) cc_final: 0.9446 (p0) REVERT: e 220 MET cc_start: 0.9247 (tmm) cc_final: 0.8905 (tmm) REVERT: e 322 MET cc_start: 0.9816 (ttm) cc_final: 0.9467 (tmm) REVERT: e 547 MET cc_start: 0.9217 (mmm) cc_final: 0.8344 (tpp) REVERT: e 704 MET cc_start: 0.8904 (ttp) cc_final: 0.8384 (tpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 1.0254 time to fit residues: 136.6229 Evaluate side-chains 87 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 249 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 262 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 7 HIS ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 229 HIS ** c 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21818 Z= 0.244 Angle : 0.565 7.435 29470 Z= 0.309 Chirality : 0.041 0.149 3315 Planarity : 0.004 0.037 3787 Dihedral : 5.334 67.977 2892 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.94 (0.16), residues: 2653 helix: 0.42 (0.18), residues: 789 sheet: -2.33 (0.19), residues: 668 loop : -1.75 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP e 63 HIS 0.010 0.001 HIS D 7 PHE 0.015 0.002 PHE d 650 TYR 0.013 0.002 TYR a 81 ARG 0.005 0.001 ARG d 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 3.780 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: D 72 ARG cc_start: 0.9826 (mtp-110) cc_final: 0.9411 (mmp80) REVERT: D 81 ASN cc_start: 0.8341 (m110) cc_final: 0.8106 (m110) REVERT: D 147 MET cc_start: 0.7025 (mmt) cc_final: 0.6288 (mmp) REVERT: d 962 ASP cc_start: 0.9743 (m-30) cc_final: 0.9437 (p0) REVERT: e 220 MET cc_start: 0.9260 (tmm) cc_final: 0.8913 (tmm) REVERT: e 251 MET cc_start: 0.9009 (tpp) cc_final: 0.8160 (mmm) REVERT: e 322 MET cc_start: 0.9820 (ttm) cc_final: 0.9456 (tmm) REVERT: e 547 MET cc_start: 0.9210 (mmm) cc_final: 0.8326 (tpp) REVERT: e 704 MET cc_start: 0.8942 (ttp) cc_final: 0.8396 (tpp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 1.0152 time to fit residues: 132.6394 Evaluate side-chains 85 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 3.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 208 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** a 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 326 GLN c 73 HIS ** c 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 332 GLN d 397 HIS ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 140 GLN ** e 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.023568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.018479 restraints weight = 1596739.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.019161 restraints weight = 1147238.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.019514 restraints weight = 829159.976| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.019 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.019 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 21818 Z= 0.384 Angle : 0.693 6.266 29470 Z= 0.385 Chirality : 0.042 0.149 3315 Planarity : 0.005 0.052 3787 Dihedral : 5.700 66.871 2892 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.15), residues: 2653 helix: -0.28 (0.17), residues: 786 sheet: -2.31 (0.19), residues: 643 loop : -2.03 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP e 533 HIS 0.010 0.002 HIS e 181 PHE 0.026 0.003 PHE d 78 TYR 0.023 0.003 TYR d 718 ARG 0.021 0.001 ARG R 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6747.87 seconds wall clock time: 123 minutes 23.04 seconds (7403.04 seconds total)