Starting phenix.real_space_refine on Wed Feb 21 11:53:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2024/7vpz_32077_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2024/7vpz_32077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2024/7vpz_32077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2024/7vpz_32077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2024/7vpz_32077_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2024/7vpz_32077_neut.pdb" } resolution = 4.14 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= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 172 5.49 5 Mg 1 5.21 5 S 100 5.16 5 C 18615 2.51 5 N 5467 2.21 5 O 6230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 184": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C ASP 587": "OD1" <-> "OD2" Residue "C GLU 718": "OE1" <-> "OE2" Residue "C GLU 739": "OE1" <-> "OE2" Residue "C GLU 888": "OE1" <-> "OE2" Residue "C PHE 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1095": "OE1" <-> "OE2" Residue "C GLU 1112": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 837": "OE1" <-> "OE2" Residue "D GLU 843": "OE1" <-> "OE2" Residue "D GLU 884": "OE1" <-> "OE2" Residue "D PHE 1209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 412": "OE1" <-> "OE2" Residue "F GLU 426": "OE1" <-> "OE2" Residue "F GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30593 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2396 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1714 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "P" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1729 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "Q" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" 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} Chain: "N" 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 12673 SG CYS D 60 79.658 104.045 123.886 1.00157.16 S ATOM 12691 SG CYS D 62 79.021 105.110 127.331 1.00153.61 S ATOM 12800 SG CYS D 75 82.700 103.851 126.399 1.00158.51 S ATOM 12826 SG CYS D 78 80.107 101.673 127.113 1.00149.86 S ATOM 19225 SG CYS D 886 107.733 49.258 92.669 1.00143.06 S ATOM 19789 SG CYS D 962 104.458 50.398 94.380 1.00126.36 S ATOM 19837 SG CYS D 969 105.139 51.933 90.988 1.00130.34 S ATOM 19856 SG CYS D 972 104.370 48.451 91.235 1.00129.45 S ATOM 25721 SG CYS M 90 77.896 161.190 48.514 1.00387.00 S ATOM 25743 SG CYS M 93 75.646 163.050 51.006 1.00382.83 S ATOM 26016 SG CYS M 130 74.193 160.628 48.385 1.00381.94 S ATOM 26035 SG CYS M 133 75.630 164.092 47.445 1.00371.66 S ATOM 25635 SG CYS M 79 79.644 148.248 57.441 1.00382.76 S ATOM 26705 SG CYS N 90 101.327 136.404 43.201 1.00397.98 S ATOM 26727 SG CYS N 93 104.918 135.407 42.086 1.00401.09 S ATOM 27000 SG CYS N 130 101.758 133.887 40.505 1.00399.20 S ATOM 27019 SG CYS N 133 102.929 133.002 44.039 1.00395.05 S ATOM 26619 SG CYS N 79 98.195 147.250 32.369 1.00384.58 S Time building chain proxies: 15.06, per 1000 atoms: 0.49 Number of scatterers: 30593 At special positions: 0 Unit cell: (136.4, 202.4, 209, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 100 16.00 P 172 15.00 Mg 1 11.99 O 6230 8.00 N 5467 7.00 C 18615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.24 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 24 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6402 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 43 sheets defined 44.1% alpha, 13.9% beta 65 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 12.06 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 4.004A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 225 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.685A pdb=" N LEU B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.504A pdb=" N THR C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.593A pdb=" N ILE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.544A pdb=" N LYS C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 removed outlier: 3.518A pdb=" N GLY C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 392 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.959A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.596A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 4.051A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 568 through 573 removed outlier: 4.656A pdb=" N MET C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 580 removed outlier: 4.111A pdb=" N ILE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 587 through 598 Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 716 through 720 removed outlier: 4.178A pdb=" N ASP C 719 " --> pdb=" O ASN C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 764 through 768 Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 911 removed outlier: 4.201A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 removed outlier: 3.605A pdb=" N LEU C 918 " --> pdb=" O PRO C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 Processing helix chain 'C' and resid 1021 through 1026 Processing helix chain 'C' and resid 1054 through 1065 Processing helix chain 'C' and resid 1066 through 1075 removed outlier: 3.517A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 4.101A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1115 removed outlier: 3.910A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.771A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 188 Processing helix chain 'D' and resid 192 through 227 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.547A pdb=" N ALA D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.591A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.582A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 360 removed outlier: 4.047A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.515A pdb=" N LEU D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.594A pdb=" N GLN D 415 " --> pdb=" O GLY D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 4.474A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.537A pdb=" N PHE D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 662 through 672 Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 4.157A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.536A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 removed outlier: 3.649A pdb=" N MET D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 876 removed outlier: 3.843A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 removed outlier: 3.889A pdb=" N SER D 914 " --> pdb=" O ASP D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 Processing helix chain 'D' and resid 970 through 974 Processing helix chain 'D' and resid 988 through 999 removed outlier: 4.102A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.300A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1108 Processing helix chain 'D' and resid 1109 through 1129 removed outlier: 4.000A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 4.126A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1208 Processing helix chain 'D' and resid 1212 through 1223 Processing helix chain 'D' and resid 1231 through 1238 Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 removed outlier: 3.670A pdb=" N LYS D1262 " --> pdb=" O THR D1258 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 removed outlier: 4.350A pdb=" N LEU E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 45 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.637A pdb=" N ILE E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 223 removed outlier: 3.872A pdb=" N ASP F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 282 Processing helix chain 'F' and resid 282 through 292 Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 325 through 346 removed outlier: 3.719A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 346 " --> pdb=" O MET F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 476 Processing helix chain 'F' and resid 482 through 498 Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.953A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 26 removed outlier: 3.510A pdb=" N VAL M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 removed outlier: 3.928A pdb=" N GLU M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 removed outlier: 3.529A pdb=" N ALA M 134 " --> pdb=" O CYS M 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 32 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 4.223A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.146A pdb=" N ALA N 134 " --> pdb=" O CYS N 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 5.486A pdb=" N GLU A 11 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 22 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL A 13 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG A 20 " --> pdb=" O VAL A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 8.019A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.770A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.889A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP B 188 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B 181 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP B 190 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU B 179 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU B 192 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 177 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 194 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR B 175 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 196 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 173 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR B 198 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 171 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 98 removed outlier: 7.502A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 50 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.618A pdb=" N GLY B 103 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 127 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 105 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.666A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.516A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY C 613 " --> pdb=" O VAL C 957 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 100 removed outlier: 6.682A pdb=" N THR C 124 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS C 98 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE C 122 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C 100 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN C 129 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C 134 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.608A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB8, first strand: chain 'C' and resid 440 through 442 removed outlier: 3.707A pdb=" N GLY C 484 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 removed outlier: 6.656A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.712A pdb=" N ASP C 566 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 628 through 629 removed outlier: 7.005A pdb=" N VAL C 628 " --> pdb=" O LEU C 688 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 634 through 639 removed outlier: 3.561A pdb=" N THR C 647 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR C 645 " --> pdb=" O GLN C 637 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL C 639 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC5, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.527A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 734 through 746 removed outlier: 5.700A pdb=" N SER C 735 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 862 " --> pdb=" O SER C 735 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N HIS C 737 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA C 860 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU C 739 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR C 858 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS C 741 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ARG C 856 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 743 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU C 854 " --> pdb=" O VAL C 743 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 745 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASN C 852 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP C 840 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 854 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 838 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG C 856 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 836 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR C 858 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS C 862 " --> pdb=" O ILE C 830 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N ILE C 830 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 754 through 755 Processing sheet with id=AC8, first strand: chain 'C' and resid 892 through 893 Processing sheet with id=AC9, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.614A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1027 through 1029 Processing sheet with id=AD2, first strand: chain 'C' and resid 1121 through 1123 removed outlier: 3.581A pdb=" N LEU D 10 " --> pdb=" O ASP D1226 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D1226 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AD4, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.411A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 336 through 337 removed outlier: 3.623A pdb=" N THR D 337 " --> pdb=" O ILE F 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 566 through 567 removed outlier: 4.098A pdb=" N ARG D 572 " --> pdb=" O LYS D 567 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AD9, first strand: chain 'D' and resid 881 through 883 Processing sheet with id=AE1, first strand: chain 'D' and resid 892 through 894 removed outlier: 4.112A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 3.533A pdb=" N GLY D1046 " --> pdb=" O VAL D1088 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE4, first strand: chain 'D' and resid 1254 through 1256 removed outlier: 3.585A pdb=" N GLU E 83 " --> pdb=" O ARG D1254 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D1256 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR E 81 " --> pdb=" O GLU D1256 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 65 through 68 Processing sheet with id=AE6, first strand: chain 'M' and resid 96 through 99 removed outlier: 5.439A pdb=" N HIS M 87 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE M 126 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS N 87 " --> pdb=" O VAL N 124 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 30 through 31 1241 hydrogen bonds defined for protein. 3522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 173 hydrogen bonds 342 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 17.27 Time building geometry restraints manager: 15.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9417 1.34 - 1.46: 5296 1.46 - 1.58: 16223 1.58 - 1.70: 342 1.70 - 1.82: 175 Bond restraints: 31453 Sorted by residual: bond pdb=" CA GLN C1040 " pdb=" C GLN C1040 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.26e-02 6.30e+03 1.01e+01 bond pdb=" O3' DG O 71 " pdb=" P DG O 72 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 1.00e+01 bond pdb=" C1' DG P 15 " pdb=" N9 DG P 15 " ideal model delta sigma weight residual 1.460 1.402 0.058 2.00e-02 2.50e+03 8.38e+00 bond pdb=" C ALA A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.81e+00 bond pdb=" N ALA D 133 " pdb=" CA ALA D 133 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.44e+00 ... (remaining 31448 not shown) Histogram of bond angle deviations from ideal: 97.64 - 105.21: 1193 105.21 - 112.78: 16970 112.78 - 120.35: 12964 120.35 - 127.91: 11680 127.91 - 135.48: 486 Bond angle restraints: 43293 Sorted by residual: angle pdb=" N GLY D 286 " pdb=" CA GLY D 286 " pdb=" C GLY D 286 " ideal model delta sigma weight residual 111.80 125.54 -13.74 1.82e+00 3.02e-01 5.70e+01 angle pdb=" N MET C1036 " pdb=" CA MET C1036 " pdb=" C MET C1036 " ideal model delta sigma weight residual 111.14 118.91 -7.77 1.08e+00 8.57e-01 5.18e+01 angle pdb=" N TYR D 134 " pdb=" CA TYR D 134 " pdb=" C TYR D 134 " ideal model delta sigma weight residual 110.55 119.65 -9.10 1.35e+00 5.49e-01 4.54e+01 angle pdb=" N TYR D 130 " pdb=" CA TYR D 130 " pdb=" C TYR D 130 " ideal model delta sigma weight residual 109.96 100.07 9.89 1.50e+00 4.44e-01 4.35e+01 angle pdb=" N ALA C 872 " pdb=" CA ALA C 872 " pdb=" C ALA C 872 " ideal model delta sigma weight residual 108.55 117.44 -8.89 1.62e+00 3.81e-01 3.01e+01 ... (remaining 43288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 17809 35.45 - 70.89: 888 70.89 - 106.34: 30 106.34 - 141.78: 4 141.78 - 177.23: 14 Dihedral angle restraints: 18745 sinusoidal: 8799 harmonic: 9946 Sorted by residual: dihedral pdb=" C LYS D 823 " pdb=" N LYS D 823 " pdb=" CA LYS D 823 " pdb=" CB LYS D 823 " ideal model delta harmonic sigma weight residual -122.60 -135.45 12.85 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N LYS D 823 " pdb=" C LYS D 823 " pdb=" CA LYS D 823 " pdb=" CB LYS D 823 " ideal model delta harmonic sigma weight residual 122.80 135.62 -12.82 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" CA ALA C 907 " pdb=" C ALA C 907 " pdb=" N VAL C 908 " pdb=" CA VAL C 908 " ideal model delta harmonic sigma weight residual 180.00 -155.92 -24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 18742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4637 0.098 - 0.196: 264 0.196 - 0.294: 19 0.294 - 0.392: 2 0.392 - 0.490: 1 Chirality restraints: 4923 Sorted by residual: chirality pdb=" CA LYS D 823 " pdb=" N LYS D 823 " pdb=" C LYS D 823 " pdb=" CB LYS D 823 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA GLN C1039 " pdb=" N GLN C1039 " pdb=" C GLN C1039 " pdb=" CB GLN C1039 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ARG C 293 " pdb=" N ARG C 293 " pdb=" C ARG C 293 " pdb=" CB ARG C 293 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 4920 not shown) Planarity restraints: 5067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 443 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO D 444 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 444 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 444 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1059 " 0.009 2.00e-02 2.50e+03 1.51e-02 5.74e+00 pdb=" CG TRP C1059 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C1059 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C1059 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C1059 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C1059 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1059 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1059 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1059 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1059 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 738 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C LYS D 738 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS D 738 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 739 " 0.013 2.00e-02 2.50e+03 ... (remaining 5064 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 202 2.49 - 3.09: 23379 3.09 - 3.69: 50724 3.69 - 4.30: 69675 4.30 - 4.90: 108837 Nonbonded interactions: 252817 Sorted by model distance: nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.887 2.230 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.903 2.230 nonbonded pdb=" O3' G Q 5 " pdb="MG MG D1401 " model vdw 1.974 2.170 nonbonded pdb=" OE2 GLU M 105 " pdb="ZN ZN M 203 " model vdw 2.066 2.230 nonbonded pdb=" OG1 THR C 339 " pdb=" OE1 GLU C 340 " model vdw 2.107 2.440 ... (remaining 252812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 13.440 Check model and map are aligned: 0.410 Set scattering table: 0.310 Process input model: 99.340 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 0.058 31453 Z= 0.288 Angle : 0.786 13.742 43293 Z= 0.458 Chirality : 0.049 0.490 4923 Planarity : 0.005 0.063 5067 Dihedral : 18.738 177.230 12343 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 0.52 % Allowed : 1.31 % Favored : 98.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3458 helix: 1.09 (0.14), residues: 1372 sheet: -0.82 (0.25), residues: 401 loop : -0.68 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C1059 HIS 0.018 0.001 HIS D 103 PHE 0.022 0.002 PHE B 219 TYR 0.026 0.002 TYR E 32 ARG 0.016 0.001 ARG C 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 543 time to evaluate : 3.349 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: A 81 LYS cc_start: 0.9134 (pptt) cc_final: 0.8784 (ptpp) REVERT: A 95 MET cc_start: 0.8532 (ttm) cc_final: 0.8185 (ttm) REVERT: A 153 LYS cc_start: 0.8252 (pttp) cc_final: 0.7570 (tptt) REVERT: B 5 GLN cc_start: 0.7335 (mp10) cc_final: 0.6899 (mp10) REVERT: B 150 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7705 (m) REVERT: C 76 GLU cc_start: 0.9253 (tm-30) cc_final: 0.9029 (tm-30) REVERT: C 269 LEU cc_start: 0.9114 (mm) cc_final: 0.8652 (tp) REVERT: C 383 GLU cc_start: 0.8485 (tt0) cc_final: 0.8234 (mt-10) REVERT: C 438 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8472 (mmtt) REVERT: C 725 GLN cc_start: 0.6764 (tm-30) cc_final: 0.6383 (tm-30) REVERT: D 19 ASP cc_start: 0.8431 (t0) cc_final: 0.8175 (t70) REVERT: D 154 HIS cc_start: 0.9428 (m90) cc_final: 0.9118 (m-70) REVERT: D 296 LEU cc_start: 0.9150 (mt) cc_final: 0.8542 (mt) REVERT: D 356 ARG cc_start: 0.8272 (tpm170) cc_final: 0.8066 (tpm170) REVERT: D 457 MET cc_start: 0.7977 (ttp) cc_final: 0.7766 (ttm) REVERT: D 470 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9233 (mmtm) REVERT: D 831 ILE cc_start: 0.9419 (mt) cc_final: 0.9012 (mt) REVERT: D 843 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8100 (mt-10) REVERT: D 881 ILE cc_start: 0.7734 (mm) cc_final: 0.7513 (mm) REVERT: D 919 MET cc_start: 0.6382 (mmm) cc_final: 0.4875 (mmp) REVERT: D 971 MET cc_start: 0.8134 (mmm) cc_final: 0.7890 (tpp) REVERT: D 1143 GLN cc_start: 0.8869 (tp40) cc_final: 0.8666 (tp40) REVERT: D 1191 MET cc_start: 0.7748 (pmm) cc_final: 0.7524 (pmm) REVERT: E 18 GLU cc_start: 0.8576 (mp0) cc_final: 0.8358 (pm20) REVERT: E 26 LYS cc_start: 0.8481 (mttt) cc_final: 0.7839 (mmmm) REVERT: E 70 ILE cc_start: 0.8844 (mp) cc_final: 0.8569 (mp) REVERT: E 75 ILE cc_start: 0.8366 (mm) cc_final: 0.8134 (mm) REVERT: F 324 TYR cc_start: 0.8104 (m-80) cc_final: 0.7802 (m-80) outliers start: 15 outliers final: 1 residues processed: 553 average time/residue: 0.4686 time to fit residues: 397.0646 Evaluate side-chains 395 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 393 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 2.9990 chunk 272 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 326 optimal weight: 50.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 152 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 921 HIS ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN D 510 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 HIS D 669 ASN D 778 ASN D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 ASN F 282 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31453 Z= 0.320 Angle : 0.685 8.446 43293 Z= 0.370 Chirality : 0.044 0.196 4923 Planarity : 0.005 0.061 5067 Dihedral : 21.011 179.372 5662 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3458 helix: 0.87 (0.13), residues: 1406 sheet: -0.78 (0.25), residues: 403 loop : -0.77 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D1203 HIS 0.006 0.001 HIS D 439 PHE 0.052 0.002 PHE D1209 TYR 0.021 0.002 TYR E 32 ARG 0.012 0.001 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 480 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8906 (ptmt) cc_final: 0.8575 (ptpp) REVERT: A 81 LYS cc_start: 0.9238 (pptt) cc_final: 0.8847 (ptpp) REVERT: A 168 TYR cc_start: 0.8588 (m-80) cc_final: 0.8014 (m-80) REVERT: B 5 GLN cc_start: 0.7363 (mp10) cc_final: 0.6970 (mp10) REVERT: B 152 ASN cc_start: 0.7495 (m-40) cc_final: 0.7242 (m-40) REVERT: C 76 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8896 (tm-30) REVERT: C 193 ILE cc_start: 0.8874 (tp) cc_final: 0.8633 (tp) REVERT: C 269 LEU cc_start: 0.9160 (mm) cc_final: 0.8713 (tp) REVERT: C 382 MET cc_start: 0.9066 (tmm) cc_final: 0.8521 (tmm) REVERT: C 383 GLU cc_start: 0.8458 (tt0) cc_final: 0.8167 (mt-10) REVERT: C 587 ASP cc_start: 0.8422 (t70) cc_final: 0.8193 (t70) REVERT: C 593 MET cc_start: 0.7799 (mmm) cc_final: 0.7429 (mmm) REVERT: C 725 GLN cc_start: 0.6919 (tm-30) cc_final: 0.6630 (tm-30) REVERT: C 807 LEU cc_start: 0.9262 (tt) cc_final: 0.8970 (pp) REVERT: C 839 PHE cc_start: 0.7781 (m-10) cc_final: 0.7439 (m-10) REVERT: C 912 MET cc_start: 0.7745 (tpt) cc_final: 0.7464 (tpt) REVERT: C 986 MET cc_start: 0.7096 (ttt) cc_final: 0.6885 (ttt) REVERT: C 1018 LEU cc_start: 0.9171 (mp) cc_final: 0.8835 (mp) REVERT: D 154 HIS cc_start: 0.9385 (m90) cc_final: 0.8981 (m90) REVERT: D 241 TYR cc_start: 0.8546 (t80) cc_final: 0.8305 (t80) REVERT: D 252 PHE cc_start: 0.8487 (p90) cc_final: 0.7724 (p90) REVERT: D 264 ARG cc_start: 0.8582 (tpm170) cc_final: 0.8325 (tpm170) REVERT: D 296 LEU cc_start: 0.9301 (mt) cc_final: 0.8818 (mt) REVERT: D 356 ARG cc_start: 0.8226 (tpm170) cc_final: 0.7968 (tpm170) REVERT: D 373 MET cc_start: 0.7126 (tpp) cc_final: 0.6389 (tpp) REVERT: D 470 LYS cc_start: 0.9477 (mmmm) cc_final: 0.9200 (mmtm) REVERT: D 475 MET cc_start: 0.9125 (tpt) cc_final: 0.6941 (tpt) REVERT: D 831 ILE cc_start: 0.9406 (mt) cc_final: 0.9132 (mt) REVERT: D 843 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8175 (mt-10) REVERT: D 919 MET cc_start: 0.6879 (mmm) cc_final: 0.4857 (mmm) REVERT: D 971 MET cc_start: 0.8370 (mmm) cc_final: 0.8102 (tpt) REVERT: D 1028 GLU cc_start: 0.8589 (tt0) cc_final: 0.8351 (tt0) REVERT: D 1134 ASP cc_start: 0.8132 (m-30) cc_final: 0.7931 (m-30) REVERT: D 1205 SER cc_start: 0.9071 (m) cc_final: 0.8856 (p) REVERT: F 229 ASN cc_start: 0.8929 (t0) cc_final: 0.8472 (p0) REVERT: F 342 MET cc_start: 0.7584 (ppp) cc_final: 0.7161 (ppp) REVERT: F 422 ILE cc_start: 0.8041 (tp) cc_final: 0.7824 (tp) outliers start: 3 outliers final: 0 residues processed: 483 average time/residue: 0.4855 time to fit residues: 361.8925 Evaluate side-chains 365 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 272 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 327 optimal weight: 50.0000 chunk 353 optimal weight: 4.9990 chunk 291 optimal weight: 0.8980 chunk 324 optimal weight: 50.0000 chunk 111 optimal weight: 0.9980 chunk 262 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 152 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 921 HIS ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31453 Z= 0.246 Angle : 0.624 8.508 43293 Z= 0.336 Chirality : 0.042 0.193 4923 Planarity : 0.005 0.095 5067 Dihedral : 20.946 179.356 5662 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3458 helix: 0.93 (0.14), residues: 1403 sheet: -0.76 (0.25), residues: 397 loop : -0.72 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 924 HIS 0.008 0.001 HIS D 849 PHE 0.040 0.002 PHE D1209 TYR 0.033 0.002 TYR E 32 ARG 0.005 0.000 ARG F 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 477 time to evaluate : 3.157 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: A 70 LYS cc_start: 0.8926 (ptmt) cc_final: 0.8605 (ptpp) REVERT: A 81 LYS cc_start: 0.9147 (pptt) cc_final: 0.8781 (ptpp) REVERT: A 168 TYR cc_start: 0.8461 (m-80) cc_final: 0.7862 (m-80) REVERT: A 202 MET cc_start: 0.8542 (pmm) cc_final: 0.8220 (pmm) REVERT: B 5 GLN cc_start: 0.7361 (mp10) cc_final: 0.6891 (mp10) REVERT: B 152 ASN cc_start: 0.7558 (m-40) cc_final: 0.7265 (m-40) REVERT: C 76 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8857 (tm-30) REVERT: C 269 LEU cc_start: 0.9157 (mm) cc_final: 0.8770 (tp) REVERT: C 356 ILE cc_start: 0.9125 (pt) cc_final: 0.8778 (pt) REVERT: C 362 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7664 (mtt-85) REVERT: C 382 MET cc_start: 0.9041 (tmm) cc_final: 0.8595 (tmm) REVERT: C 383 GLU cc_start: 0.8466 (tt0) cc_final: 0.8187 (mt-10) REVERT: C 593 MET cc_start: 0.7747 (mmm) cc_final: 0.7538 (mmm) REVERT: C 701 LEU cc_start: 0.8722 (mp) cc_final: 0.8340 (mp) REVERT: C 725 GLN cc_start: 0.6723 (tm-30) cc_final: 0.6312 (tm-30) REVERT: C 1018 LEU cc_start: 0.9191 (mp) cc_final: 0.8815 (mp) REVERT: D 154 HIS cc_start: 0.9369 (m90) cc_final: 0.8981 (m90) REVERT: D 264 ARG cc_start: 0.8572 (tpm170) cc_final: 0.8324 (tpm170) REVERT: D 296 LEU cc_start: 0.9169 (mt) cc_final: 0.8630 (mt) REVERT: D 314 LEU cc_start: 0.8152 (pt) cc_final: 0.7895 (pt) REVERT: D 356 ARG cc_start: 0.8173 (tpm170) cc_final: 0.7863 (tpm170) REVERT: D 449 LEU cc_start: 0.8950 (mt) cc_final: 0.8739 (mt) REVERT: D 457 MET cc_start: 0.7282 (ttt) cc_final: 0.7016 (tpp) REVERT: D 843 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8053 (mt-10) REVERT: D 919 MET cc_start: 0.6896 (mmm) cc_final: 0.5945 (mmm) REVERT: D 971 MET cc_start: 0.8378 (mmm) cc_final: 0.7896 (mmm) REVERT: D 1028 GLU cc_start: 0.8525 (tt0) cc_final: 0.8292 (tt0) REVERT: F 229 ASN cc_start: 0.8954 (t0) cc_final: 0.8436 (p0) REVERT: F 342 MET cc_start: 0.7583 (ppp) cc_final: 0.7208 (ppp) outliers start: 1 outliers final: 0 residues processed: 478 average time/residue: 0.4571 time to fit residues: 338.6032 Evaluate side-chains 351 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 30.0000 chunk 246 optimal weight: 0.0030 chunk 169 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 219 optimal weight: 0.0070 chunk 328 optimal weight: 40.0000 chunk 347 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 152 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 741 HIS C 921 HIS ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN D 767 GLN D 778 ASN D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1182 HIS ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31453 Z= 0.304 Angle : 0.657 9.012 43293 Z= 0.354 Chirality : 0.043 0.266 4923 Planarity : 0.005 0.087 5067 Dihedral : 20.921 179.937 5662 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3458 helix: 0.79 (0.14), residues: 1399 sheet: -0.85 (0.24), residues: 418 loop : -0.84 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 924 HIS 0.006 0.001 HIS D 849 PHE 0.023 0.002 PHE D 512 TYR 0.028 0.002 TYR E 32 ARG 0.020 0.001 ARG D 810 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 3.355 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: A 106 THR cc_start: 0.7583 (p) cc_final: 0.7191 (t) REVERT: A 168 TYR cc_start: 0.8570 (m-80) cc_final: 0.7901 (m-80) REVERT: B 5 GLN cc_start: 0.7483 (mp10) cc_final: 0.7202 (mp10) REVERT: B 202 MET cc_start: 0.8239 (mtt) cc_final: 0.7979 (mtm) REVERT: C 76 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8911 (tm-30) REVERT: C 269 LEU cc_start: 0.9174 (mm) cc_final: 0.8787 (tp) REVERT: C 382 MET cc_start: 0.9053 (tmm) cc_final: 0.8766 (tmm) REVERT: C 587 ASP cc_start: 0.8682 (t0) cc_final: 0.8389 (t0) REVERT: C 593 MET cc_start: 0.7759 (mmm) cc_final: 0.7535 (mmm) REVERT: C 725 GLN cc_start: 0.7152 (tm-30) cc_final: 0.6710 (tm-30) REVERT: C 1018 LEU cc_start: 0.9267 (mp) cc_final: 0.8930 (mp) REVERT: D 19 ASP cc_start: 0.8602 (t0) cc_final: 0.8396 (t70) REVERT: D 154 HIS cc_start: 0.9406 (m90) cc_final: 0.8963 (m90) REVERT: D 264 ARG cc_start: 0.8695 (tpm170) cc_final: 0.7831 (tpm170) REVERT: D 296 LEU cc_start: 0.9248 (mt) cc_final: 0.8675 (mt) REVERT: D 310 LYS cc_start: 0.9348 (pptt) cc_final: 0.8949 (pptt) REVERT: D 356 ARG cc_start: 0.8244 (tpm170) cc_final: 0.7867 (tpm170) REVERT: D 405 MET cc_start: 0.7958 (tpp) cc_final: 0.7449 (mmt) REVERT: D 457 MET cc_start: 0.7474 (ttt) cc_final: 0.7036 (tpp) REVERT: D 843 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8067 (mt-10) REVERT: D 971 MET cc_start: 0.8394 (mmm) cc_final: 0.7653 (tpp) REVERT: D 1028 GLU cc_start: 0.8529 (tt0) cc_final: 0.8197 (tt0) REVERT: F 229 ASN cc_start: 0.8956 (t0) cc_final: 0.8479 (p0) REVERT: F 342 MET cc_start: 0.7735 (ppp) cc_final: 0.7349 (ppp) REVERT: F 355 MET cc_start: 0.8591 (tpt) cc_final: 0.8038 (tpp) REVERT: F 422 ILE cc_start: 0.8267 (tp) cc_final: 0.8018 (tp) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.4644 time to fit residues: 320.3643 Evaluate side-chains 341 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 296 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 89 HIS ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN C 741 HIS D 710 ASN D 778 ASN D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31453 Z= 0.292 Angle : 0.646 9.454 43293 Z= 0.347 Chirality : 0.043 0.225 4923 Planarity : 0.005 0.074 5067 Dihedral : 20.903 179.662 5662 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3458 helix: 0.83 (0.14), residues: 1396 sheet: -0.85 (0.24), residues: 422 loop : -0.81 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C1059 HIS 0.007 0.001 HIS D 849 PHE 0.019 0.002 PHE C 154 TYR 0.028 0.002 TYR E 32 ARG 0.011 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 3.368 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: A 106 THR cc_start: 0.7680 (p) cc_final: 0.7335 (t) REVERT: A 168 TYR cc_start: 0.8472 (m-80) cc_final: 0.7725 (m-80) REVERT: B 5 GLN cc_start: 0.7454 (mp10) cc_final: 0.7219 (mp10) REVERT: C 76 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8903 (tm-30) REVERT: C 148 MET cc_start: 0.8686 (tpt) cc_final: 0.8335 (tpt) REVERT: C 201 GLU cc_start: 0.7223 (mp0) cc_final: 0.6841 (mp0) REVERT: C 382 MET cc_start: 0.9045 (tmm) cc_final: 0.8691 (tmm) REVERT: C 383 GLU cc_start: 0.8407 (tt0) cc_final: 0.8161 (mt-10) REVERT: C 587 ASP cc_start: 0.8507 (t0) cc_final: 0.8270 (t0) REVERT: D 19 ASP cc_start: 0.8580 (t0) cc_final: 0.8373 (t70) REVERT: D 134 TYR cc_start: 0.8279 (m-10) cc_final: 0.7987 (m-80) REVERT: D 256 MET cc_start: 0.6644 (tpp) cc_final: 0.6437 (tpp) REVERT: D 264 ARG cc_start: 0.8697 (tpm170) cc_final: 0.7665 (tpm170) REVERT: D 296 LEU cc_start: 0.9306 (mt) cc_final: 0.8768 (mt) REVERT: D 356 ARG cc_start: 0.8257 (tpm170) cc_final: 0.7869 (tpm170) REVERT: D 405 MET cc_start: 0.7992 (tpp) cc_final: 0.7532 (mmt) REVERT: D 449 LEU cc_start: 0.8888 (mt) cc_final: 0.8686 (mt) REVERT: D 457 MET cc_start: 0.7446 (ttt) cc_final: 0.6949 (tpp) REVERT: D 590 THR cc_start: 0.6281 (m) cc_final: 0.6062 (m) REVERT: D 831 ILE cc_start: 0.9373 (mt) cc_final: 0.9160 (mp) REVERT: D 843 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8292 (mt-10) REVERT: D 884 GLU cc_start: 0.7372 (pm20) cc_final: 0.7130 (pm20) REVERT: D 919 MET cc_start: 0.6992 (mmm) cc_final: 0.5318 (mmm) REVERT: D 971 MET cc_start: 0.8339 (mmm) cc_final: 0.8030 (tpt) REVERT: D 1028 GLU cc_start: 0.8461 (tt0) cc_final: 0.8120 (tt0) REVERT: D 1224 LYS cc_start: 0.8075 (pptt) cc_final: 0.7682 (mmmt) REVERT: E 72 LEU cc_start: 0.8721 (tp) cc_final: 0.8379 (pp) REVERT: E 79 LEU cc_start: 0.8563 (mp) cc_final: 0.8075 (tt) REVERT: F 229 ASN cc_start: 0.9096 (t0) cc_final: 0.8567 (p0) REVERT: F 342 MET cc_start: 0.7981 (ppp) cc_final: 0.7541 (ppp) REVERT: F 355 MET cc_start: 0.8618 (tpt) cc_final: 0.8022 (tpp) REVERT: F 422 ILE cc_start: 0.8330 (tp) cc_final: 0.8079 (tp) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.4767 time to fit residues: 320.8159 Evaluate side-chains 332 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.8980 chunk 313 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN C 361 ASN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31453 Z= 0.333 Angle : 0.678 9.355 43293 Z= 0.365 Chirality : 0.044 0.200 4923 Planarity : 0.005 0.066 5067 Dihedral : 20.889 179.599 5662 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3458 helix: 0.65 (0.14), residues: 1412 sheet: -0.86 (0.25), residues: 413 loop : -0.92 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 924 HIS 0.009 0.001 HIS C 465 PHE 0.030 0.002 PHE D 248 TYR 0.036 0.002 TYR C1014 ARG 0.012 0.001 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 3.486 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: A 70 LYS cc_start: 0.8966 (pttm) cc_final: 0.8566 (ptpp) REVERT: C 76 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8932 (tm-30) REVERT: C 148 MET cc_start: 0.8556 (tpt) cc_final: 0.8162 (tpt) REVERT: C 382 MET cc_start: 0.9016 (tmm) cc_final: 0.8736 (tmm) REVERT: C 587 ASP cc_start: 0.8653 (t0) cc_final: 0.8383 (t0) REVERT: C 710 MET cc_start: 0.8628 (ppp) cc_final: 0.8361 (ppp) REVERT: D 19 ASP cc_start: 0.8642 (t0) cc_final: 0.8435 (t70) REVERT: D 30 LYS cc_start: 0.9046 (tptm) cc_final: 0.8632 (tptm) REVERT: D 92 MET cc_start: 0.6895 (pmm) cc_final: 0.6693 (pmm) REVERT: D 134 TYR cc_start: 0.8066 (m-10) cc_final: 0.7662 (m-80) REVERT: D 256 MET cc_start: 0.5252 (ttm) cc_final: 0.5040 (ttm) REVERT: D 310 LYS cc_start: 0.9305 (pptt) cc_final: 0.8975 (pptt) REVERT: D 314 LEU cc_start: 0.8290 (pt) cc_final: 0.8075 (pt) REVERT: D 356 ARG cc_start: 0.8246 (tpm170) cc_final: 0.7880 (tpm170) REVERT: D 405 MET cc_start: 0.7973 (tpp) cc_final: 0.7581 (mmt) REVERT: D 457 MET cc_start: 0.7350 (ttt) cc_final: 0.6894 (tpp) REVERT: D 809 MET cc_start: 0.8355 (ttm) cc_final: 0.8113 (ttm) REVERT: D 919 MET cc_start: 0.7661 (mmm) cc_final: 0.5909 (mmt) REVERT: D 971 MET cc_start: 0.8378 (mmm) cc_final: 0.8137 (tpt) REVERT: D 1028 GLU cc_start: 0.8456 (tt0) cc_final: 0.8110 (tt0) REVERT: D 1224 LYS cc_start: 0.8212 (pptt) cc_final: 0.7957 (mmmt) REVERT: E 79 LEU cc_start: 0.8597 (mp) cc_final: 0.8102 (tt) REVERT: F 229 ASN cc_start: 0.9107 (t0) cc_final: 0.8642 (p0) REVERT: F 299 LEU cc_start: 0.8366 (mm) cc_final: 0.8148 (mm) REVERT: F 342 MET cc_start: 0.8045 (ppp) cc_final: 0.7523 (ppp) REVERT: F 355 MET cc_start: 0.8549 (tpt) cc_final: 0.8166 (tpt) REVERT: F 422 ILE cc_start: 0.8329 (tp) cc_final: 0.8028 (tp) REVERT: F 432 ASP cc_start: 0.9093 (m-30) cc_final: 0.8740 (m-30) REVERT: F 492 LYS cc_start: 0.9596 (mmmm) cc_final: 0.9376 (mmmm) REVERT: F 494 MET cc_start: 0.9028 (mmt) cc_final: 0.8740 (mmt) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.4603 time to fit residues: 294.2676 Evaluate side-chains 316 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 197 optimal weight: 0.4980 chunk 293 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 346 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 160 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31453 Z= 0.191 Angle : 0.618 8.367 43293 Z= 0.329 Chirality : 0.042 0.218 4923 Planarity : 0.004 0.054 5067 Dihedral : 20.761 179.174 5662 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3458 helix: 0.95 (0.14), residues: 1399 sheet: -0.81 (0.24), residues: 424 loop : -0.74 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 924 HIS 0.010 0.001 HIS D 849 PHE 0.022 0.002 PHE D 302 TYR 0.026 0.001 TYR E 32 ARG 0.007 0.000 ARG D 810 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 3.434 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: A 41 THR cc_start: 0.8078 (m) cc_final: 0.7874 (t) REVERT: A 70 LYS cc_start: 0.8932 (pttm) cc_final: 0.8652 (ptpp) REVERT: A 168 TYR cc_start: 0.8515 (m-80) cc_final: 0.7928 (m-80) REVERT: B 82 GLN cc_start: 0.8668 (tt0) cc_final: 0.7996 (pt0) REVERT: C 76 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8749 (tm-30) REVERT: C 201 GLU cc_start: 0.7285 (mp0) cc_final: 0.6893 (mp0) REVERT: C 382 MET cc_start: 0.8993 (tmm) cc_final: 0.8689 (tmm) REVERT: C 383 GLU cc_start: 0.8424 (tt0) cc_final: 0.8195 (mt-10) REVERT: C 565 MET cc_start: 0.6925 (ppp) cc_final: 0.5969 (ppp) REVERT: C 573 VAL cc_start: 0.8741 (m) cc_final: 0.8360 (p) REVERT: C 587 ASP cc_start: 0.8491 (t0) cc_final: 0.8254 (t0) REVERT: C 1071 GLN cc_start: 0.7214 (tt0) cc_final: 0.6994 (mm-40) REVERT: D 19 ASP cc_start: 0.8567 (t0) cc_final: 0.8257 (t0) REVERT: D 30 LYS cc_start: 0.9030 (tptm) cc_final: 0.8639 (tptm) REVERT: D 134 TYR cc_start: 0.8072 (m-80) cc_final: 0.7708 (m-80) REVERT: D 310 LYS cc_start: 0.9191 (pptt) cc_final: 0.8893 (pptt) REVERT: D 314 LEU cc_start: 0.8065 (pt) cc_final: 0.7848 (pt) REVERT: D 356 ARG cc_start: 0.8291 (tpm170) cc_final: 0.7876 (tpm170) REVERT: D 373 MET cc_start: 0.7254 (tpp) cc_final: 0.6871 (tpp) REVERT: D 457 MET cc_start: 0.7480 (ttt) cc_final: 0.6817 (tpp) REVERT: D 590 THR cc_start: 0.5765 (m) cc_final: 0.5538 (m) REVERT: D 919 MET cc_start: 0.7571 (mmm) cc_final: 0.7085 (mmm) REVERT: D 1028 GLU cc_start: 0.8298 (tt0) cc_final: 0.7991 (tt0) REVERT: D 1224 LYS cc_start: 0.7954 (pptt) cc_final: 0.7687 (mmmt) REVERT: E 79 LEU cc_start: 0.8394 (mp) cc_final: 0.7960 (tt) REVERT: F 229 ASN cc_start: 0.9018 (t0) cc_final: 0.8579 (p0) REVERT: F 324 TYR cc_start: 0.8004 (m-80) cc_final: 0.7690 (m-80) REVERT: F 342 MET cc_start: 0.8017 (ppp) cc_final: 0.7494 (ppp) REVERT: F 355 MET cc_start: 0.8405 (tpt) cc_final: 0.7978 (tpt) REVERT: F 422 ILE cc_start: 0.8278 (tp) cc_final: 0.8012 (tp) REVERT: F 432 ASP cc_start: 0.9028 (m-30) cc_final: 0.8649 (m-30) REVERT: F 494 MET cc_start: 0.8992 (mmt) cc_final: 0.8720 (mmt) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.4592 time to fit residues: 313.9092 Evaluate side-chains 337 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 HIS ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31453 Z= 0.284 Angle : 0.652 8.812 43293 Z= 0.349 Chirality : 0.043 0.301 4923 Planarity : 0.005 0.057 5067 Dihedral : 20.786 179.146 5662 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3458 helix: 0.92 (0.14), residues: 1392 sheet: -0.74 (0.25), residues: 421 loop : -0.86 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 924 HIS 0.010 0.001 HIS D 849 PHE 0.020 0.002 PHE D1209 TYR 0.024 0.002 TYR D 106 ARG 0.017 0.001 ARG D 810 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 3.186 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: A 41 THR cc_start: 0.8160 (m) cc_final: 0.7932 (t) REVERT: A 70 LYS cc_start: 0.8959 (pttm) cc_final: 0.8757 (ptpp) REVERT: B 82 GLN cc_start: 0.8790 (tt0) cc_final: 0.8096 (pt0) REVERT: C 76 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8946 (tm-30) REVERT: C 148 MET cc_start: 0.8360 (tpt) cc_final: 0.7869 (tpt) REVERT: C 382 MET cc_start: 0.8980 (tmm) cc_final: 0.8669 (tmm) REVERT: C 383 GLU cc_start: 0.8397 (tt0) cc_final: 0.8157 (mt-10) REVERT: C 480 ILE cc_start: 0.9157 (tp) cc_final: 0.8854 (tt) REVERT: C 587 ASP cc_start: 0.8670 (t0) cc_final: 0.8401 (t0) REVERT: C 598 MET cc_start: 0.6892 (ttt) cc_final: 0.6668 (ttt) REVERT: D 19 ASP cc_start: 0.8630 (t0) cc_final: 0.8353 (t70) REVERT: D 30 LYS cc_start: 0.9044 (tptm) cc_final: 0.8588 (tptm) REVERT: D 134 TYR cc_start: 0.8081 (m-80) cc_final: 0.7663 (m-80) REVERT: D 302 PHE cc_start: 0.7893 (m-10) cc_final: 0.7570 (m-80) REVERT: D 356 ARG cc_start: 0.8281 (tpm170) cc_final: 0.7883 (tpm170) REVERT: D 405 MET cc_start: 0.7754 (mmt) cc_final: 0.7348 (mmt) REVERT: D 457 MET cc_start: 0.7491 (ttt) cc_final: 0.6965 (tpp) REVERT: D 612 MET cc_start: 0.9195 (tpp) cc_final: 0.8974 (mmm) REVERT: D 808 GLN cc_start: 0.8776 (mp10) cc_final: 0.8398 (mp10) REVERT: D 809 MET cc_start: 0.8389 (ttp) cc_final: 0.8150 (ttt) REVERT: D 919 MET cc_start: 0.7550 (mmm) cc_final: 0.7000 (mmt) REVERT: D 1028 GLU cc_start: 0.8282 (tt0) cc_final: 0.8043 (tt0) REVERT: D 1224 LYS cc_start: 0.8050 (pptt) cc_final: 0.7779 (mmmt) REVERT: F 229 ASN cc_start: 0.9075 (t0) cc_final: 0.8816 (t0) REVERT: F 299 LEU cc_start: 0.8571 (mm) cc_final: 0.8340 (mm) REVERT: F 324 TYR cc_start: 0.8143 (m-80) cc_final: 0.7832 (m-80) REVERT: F 342 MET cc_start: 0.8004 (ppp) cc_final: 0.7530 (ppp) REVERT: F 355 MET cc_start: 0.8488 (tpt) cc_final: 0.8176 (tpt) REVERT: F 422 ILE cc_start: 0.8311 (tp) cc_final: 0.8053 (tp) REVERT: F 432 ASP cc_start: 0.9043 (m-30) cc_final: 0.8696 (m-30) REVERT: F 436 PHE cc_start: 0.9215 (t80) cc_final: 0.8962 (t80) REVERT: F 492 LYS cc_start: 0.9608 (mmmm) cc_final: 0.9386 (mmmm) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.4519 time to fit residues: 292.0667 Evaluate side-chains 322 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 1.9990 chunk 332 optimal weight: 8.9990 chunk 303 optimal weight: 0.9990 chunk 323 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 99 optimal weight: 0.3980 chunk 292 optimal weight: 20.0000 chunk 305 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31453 Z= 0.228 Angle : 0.634 9.302 43293 Z= 0.336 Chirality : 0.042 0.285 4923 Planarity : 0.004 0.049 5067 Dihedral : 20.754 178.390 5662 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3458 helix: 0.96 (0.14), residues: 1389 sheet: -0.68 (0.25), residues: 406 loop : -0.75 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 924 HIS 0.011 0.001 HIS D 849 PHE 0.019 0.002 PHE B 63 TYR 0.024 0.002 TYR D 106 ARG 0.010 0.000 ARG D 810 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 3.315 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: A 41 THR cc_start: 0.8140 (m) cc_final: 0.7934 (t) REVERT: A 70 LYS cc_start: 0.8923 (pttm) cc_final: 0.8722 (ptpp) REVERT: A 168 TYR cc_start: 0.8474 (m-80) cc_final: 0.7797 (m-80) REVERT: A 173 LYS cc_start: 0.7570 (ptmt) cc_final: 0.7252 (ttmt) REVERT: B 5 GLN cc_start: 0.7859 (mp10) cc_final: 0.7626 (mp10) REVERT: B 82 GLN cc_start: 0.8807 (tt0) cc_final: 0.8090 (pt0) REVERT: C 76 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8910 (tm-30) REVERT: C 148 MET cc_start: 0.8222 (tpt) cc_final: 0.7667 (tpt) REVERT: C 382 MET cc_start: 0.8965 (tmm) cc_final: 0.8664 (tmm) REVERT: C 383 GLU cc_start: 0.8417 (tt0) cc_final: 0.8190 (mt-10) REVERT: C 480 ILE cc_start: 0.9050 (tp) cc_final: 0.8709 (tt) REVERT: C 573 VAL cc_start: 0.8655 (m) cc_final: 0.8308 (p) REVERT: C 587 ASP cc_start: 0.8595 (t0) cc_final: 0.8332 (t0) REVERT: C 593 MET cc_start: 0.7918 (mmm) cc_final: 0.7616 (mmm) REVERT: C 598 MET cc_start: 0.6813 (ttt) cc_final: 0.6598 (ttt) REVERT: D 19 ASP cc_start: 0.8594 (t0) cc_final: 0.8267 (t0) REVERT: D 30 LYS cc_start: 0.9039 (tptm) cc_final: 0.8604 (tptm) REVERT: D 92 MET cc_start: 0.7057 (pmm) cc_final: 0.6622 (pmm) REVERT: D 113 ARG cc_start: 0.7501 (ptt180) cc_final: 0.6607 (mmm160) REVERT: D 134 TYR cc_start: 0.7990 (m-80) cc_final: 0.7479 (m-80) REVERT: D 296 LEU cc_start: 0.9149 (mt) cc_final: 0.8942 (mt) REVERT: D 356 ARG cc_start: 0.8224 (tpm170) cc_final: 0.7846 (tpm170) REVERT: D 405 MET cc_start: 0.7750 (mmt) cc_final: 0.7225 (mmt) REVERT: D 457 MET cc_start: 0.7487 (ttt) cc_final: 0.6844 (tpp) REVERT: D 590 THR cc_start: 0.6138 (m) cc_final: 0.5925 (m) REVERT: D 808 GLN cc_start: 0.8762 (mp10) cc_final: 0.8404 (mp10) REVERT: D 809 MET cc_start: 0.8440 (ttp) cc_final: 0.8107 (ttt) REVERT: D 919 MET cc_start: 0.7552 (mmm) cc_final: 0.6952 (mmt) REVERT: D 1028 GLU cc_start: 0.8226 (tt0) cc_final: 0.8016 (tt0) REVERT: F 229 ASN cc_start: 0.9056 (t0) cc_final: 0.8799 (t0) REVERT: F 299 LEU cc_start: 0.8690 (mm) cc_final: 0.8488 (mm) REVERT: F 324 TYR cc_start: 0.8168 (m-80) cc_final: 0.7870 (m-80) REVERT: F 342 MET cc_start: 0.8010 (ppp) cc_final: 0.7523 (ppp) REVERT: F 355 MET cc_start: 0.8484 (tpt) cc_final: 0.8171 (tpt) REVERT: F 422 ILE cc_start: 0.8317 (tp) cc_final: 0.8073 (tp) REVERT: F 432 ASP cc_start: 0.9033 (m-30) cc_final: 0.8657 (m-30) REVERT: F 436 PHE cc_start: 0.9171 (t80) cc_final: 0.8938 (t80) REVERT: F 492 LYS cc_start: 0.9617 (mmmm) cc_final: 0.9390 (mmmm) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.4701 time to fit residues: 299.1756 Evaluate side-chains 325 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.0070 chunk 341 optimal weight: 0.0770 chunk 208 optimal weight: 0.9980 chunk 162 optimal weight: 20.0000 chunk 237 optimal weight: 7.9990 chunk 358 optimal weight: 30.0000 chunk 330 optimal weight: 50.0000 chunk 285 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 overall best weight: 1.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31453 Z= 0.231 Angle : 0.632 9.240 43293 Z= 0.335 Chirality : 0.042 0.287 4923 Planarity : 0.004 0.049 5067 Dihedral : 20.715 178.403 5662 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3458 helix: 0.95 (0.14), residues: 1397 sheet: -0.64 (0.26), residues: 406 loop : -0.74 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 924 HIS 0.011 0.001 HIS D 849 PHE 0.019 0.002 PHE B 63 TYR 0.025 0.001 TYR D 106 ARG 0.010 0.000 ARG D 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 3.497 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: A 70 LYS cc_start: 0.8971 (pttm) cc_final: 0.8752 (ptpp) REVERT: A 168 TYR cc_start: 0.8435 (m-80) cc_final: 0.7743 (m-80) REVERT: B 82 GLN cc_start: 0.8802 (tt0) cc_final: 0.8108 (pt0) REVERT: C 76 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8956 (tm-30) REVERT: C 148 MET cc_start: 0.8221 (tpt) cc_final: 0.7656 (tpt) REVERT: C 382 MET cc_start: 0.8986 (tmm) cc_final: 0.8688 (tmm) REVERT: C 383 GLU cc_start: 0.8431 (tt0) cc_final: 0.8204 (mt-10) REVERT: C 480 ILE cc_start: 0.9088 (tp) cc_final: 0.8736 (tt) REVERT: C 573 VAL cc_start: 0.8617 (m) cc_final: 0.8278 (p) REVERT: C 587 ASP cc_start: 0.8648 (t0) cc_final: 0.8277 (t0) REVERT: C 593 MET cc_start: 0.7908 (mmm) cc_final: 0.7649 (mmm) REVERT: C 598 MET cc_start: 0.6787 (ttt) cc_final: 0.6549 (ttt) REVERT: D 19 ASP cc_start: 0.8608 (t0) cc_final: 0.8309 (t0) REVERT: D 30 LYS cc_start: 0.9027 (tptm) cc_final: 0.8601 (tptm) REVERT: D 92 MET cc_start: 0.7058 (pmm) cc_final: 0.6604 (pmm) REVERT: D 113 ARG cc_start: 0.7526 (ptt180) cc_final: 0.6586 (mmm160) REVERT: D 134 TYR cc_start: 0.7982 (m-80) cc_final: 0.7522 (m-80) REVERT: D 296 LEU cc_start: 0.9131 (mt) cc_final: 0.8902 (mt) REVERT: D 356 ARG cc_start: 0.8273 (tpm170) cc_final: 0.7862 (tpm170) REVERT: D 405 MET cc_start: 0.7735 (mmt) cc_final: 0.7188 (mmt) REVERT: D 457 MET cc_start: 0.7478 (ttt) cc_final: 0.6928 (tpp) REVERT: D 590 THR cc_start: 0.6270 (m) cc_final: 0.6060 (m) REVERT: D 808 GLN cc_start: 0.8770 (mp10) cc_final: 0.8389 (mp10) REVERT: D 809 MET cc_start: 0.8457 (ttp) cc_final: 0.8082 (ttt) REVERT: D 864 ASP cc_start: 0.8571 (m-30) cc_final: 0.8359 (m-30) REVERT: D 919 MET cc_start: 0.7538 (mmm) cc_final: 0.6927 (mmt) REVERT: D 1028 GLU cc_start: 0.8245 (tt0) cc_final: 0.8002 (tt0) REVERT: F 229 ASN cc_start: 0.9059 (t0) cc_final: 0.8802 (t0) REVERT: F 342 MET cc_start: 0.7991 (ppp) cc_final: 0.7556 (ppp) REVERT: F 355 MET cc_start: 0.8446 (tpt) cc_final: 0.8192 (tpt) REVERT: F 406 LEU cc_start: 0.4895 (mp) cc_final: 0.4600 (mp) REVERT: F 422 ILE cc_start: 0.8316 (tp) cc_final: 0.8058 (tp) REVERT: F 432 ASP cc_start: 0.9044 (m-30) cc_final: 0.8671 (m-30) REVERT: F 492 LYS cc_start: 0.9616 (mmmm) cc_final: 0.9390 (mmmm) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.4505 time to fit residues: 289.1517 Evaluate side-chains 319 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 2.9990 chunk 304 optimal weight: 0.0770 chunk 87 optimal weight: 2.9990 chunk 263 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 293 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN B 151 GLN ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 HIS ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.130512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092734 restraints weight = 113217.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.093270 restraints weight = 79960.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093540 restraints weight = 66107.942| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31453 Z= 0.234 Angle : 0.636 11.551 43293 Z= 0.335 Chirality : 0.042 0.283 4923 Planarity : 0.005 0.051 5067 Dihedral : 20.695 178.593 5662 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3458 helix: 0.95 (0.14), residues: 1403 sheet: -0.69 (0.25), residues: 411 loop : -0.74 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 924 HIS 0.011 0.001 HIS D 849 PHE 0.021 0.002 PHE B 63 TYR 0.021 0.001 TYR D 844 ARG 0.008 0.000 ARG D 810 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6719.47 seconds wall clock time: 123 minutes 52.55 seconds (7432.55 seconds total)