Starting phenix.real_space_refine on Sun Feb 18 11:56:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glm_40199/02_2024/8glm_40199_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glm_40199/02_2024/8glm_40199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glm_40199/02_2024/8glm_40199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glm_40199/02_2024/8glm_40199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glm_40199/02_2024/8glm_40199_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glm_40199/02_2024/8glm_40199_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 13844 2.51 5 N 3668 2.21 5 O 4343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ASP 730": "OD1" <-> "OD2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A TYR 874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "A ASP 948": "OD1" <-> "OD2" Residue "A ASP 1055": "OD1" <-> "OD2" Residue "A ASP 1083": "OD1" <-> "OD2" Residue "A GLU 1130": "OE1" <-> "OE2" Residue "A GLU 1176": "OE1" <-> "OE2" Residue "A ASP 1180": "OD1" <-> "OD2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A GLU 1197": "OE1" <-> "OE2" Residue "A ASP 1232": "OD1" <-> "OD2" Residue "A PHE 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1280": "OD1" <-> "OD2" Residue "A ASP 1286": "OD1" <-> "OD2" Residue "A ASP 1377": "OD1" <-> "OD2" Residue "A PHE 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1414": "OD1" <-> "OD2" Residue "A ASP 1424": "OD1" <-> "OD2" Residue "A ASP 1526": "OD1" <-> "OD2" Residue "A GLU 1555": "OE1" <-> "OE2" Residue "A TYR 1588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1592": "OE1" <-> "OE2" Residue "A GLU 1593": "OE1" <-> "OE2" Residue "A ASP 1600": "OD1" <-> "OD2" Residue "A ASP 1609": "OD1" <-> "OD2" Residue "A GLU 1680": "OE1" <-> "OE2" Residue "A TYR 1692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1809": "OD1" <-> "OD2" Residue "A GLU 1861": "OE1" <-> "OE2" Residue "A GLU 1863": "OE1" <-> "OE2" Residue "A TYR 1952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1985": "OD1" <-> "OD2" Residue "A ASP 2034": "OD1" <-> "OD2" Residue "A GLU 2053": "OE1" <-> "OE2" Residue "A TYR 2062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2081": "OE1" <-> "OE2" Residue "A GLU 2125": "OE1" <-> "OE2" Residue "A ASP 2127": "OD1" <-> "OD2" Residue "A PHE 2175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2237": "OE1" <-> "OE2" Residue "A PHE 2249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2291": "OE1" <-> "OE2" Residue "A GLU 2333": "OE1" <-> "OE2" Residue "A ASP 2340": "OD1" <-> "OD2" Residue "A ASP 2360": "OD1" <-> "OD2" Residue "A TYR 2361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F ASP 173": "OD1" <-> "OD2" Residue "F ASP 197": "OD1" <-> "OD2" Residue "F ASP 221": "OD1" <-> "OD2" Residue "F ASP 243": "OD1" <-> "OD2" Residue "F TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 400": "OE1" <-> "OE2" Residue "D TYR 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1057": "OD1" <-> "OD2" Residue "D TYR 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1079": "OE1" <-> "OE2" Residue "D ASP 1102": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21902 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2191, 17380 Classifications: {'peptide': 2191} Link IDs: {'PCIS': 3, 'PTRANS': 99, 'TRANS': 2088} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.22, per 1000 atoms: 0.51 Number of scatterers: 21902 At special positions: 0 Unit cell: (118.976, 128.128, 134.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 4343 8.00 N 3668 7.00 C 13844 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: 8.30 Conformation dependent library (CDL) restraints added in 4.1 seconds 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 29 sheets defined 11.3% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.58 Creating SS restraints... Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.677A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 518 through 522 removed outlier: 3.570A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 522' Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 651 through 654 No H-bonds generated for 'chain 'A' and resid 651 through 654' Processing helix chain 'A' and resid 658 through 661 No H-bonds generated for 'chain 'A' and resid 658 through 661' Processing helix chain 'A' and resid 664 through 669 removed outlier: 4.095A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 811 through 819 Processing helix chain 'A' and resid 846 through 848 No H-bonds generated for 'chain 'A' and resid 846 through 848' Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 899 through 902 Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.700A pdb=" N SER A 919 " --> pdb=" O VAL A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 943 No H-bonds generated for 'chain 'A' and resid 940 through 943' Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 999 through 1002 No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1082 through 1088 Processing helix chain 'A' and resid 1100 through 1103 No H-bonds generated for 'chain 'A' and resid 1100 through 1103' Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1121 through 1123 No H-bonds generated for 'chain 'A' and resid 1121 through 1123' Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'A' and resid 1413 through 1416 No H-bonds generated for 'chain 'A' and resid 1413 through 1416' Processing helix chain 'A' and resid 1419 through 1421 No H-bonds generated for 'chain 'A' and resid 1419 through 1421' Processing helix chain 'A' and resid 1427 through 1439 removed outlier: 4.117A pdb=" N SER A1439 " --> pdb=" O ILE A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1457 No H-bonds generated for 'chain 'A' and resid 1455 through 1457' Processing helix chain 'A' and resid 1572 through 1575 Processing helix chain 'A' and resid 1608 through 1613 Processing helix chain 'A' and resid 1618 through 1627 Processing helix chain 'A' and resid 1657 through 1659 No H-bonds generated for 'chain 'A' and resid 1657 through 1659' Processing helix chain 'A' and resid 1831 through 1833 No H-bonds generated for 'chain 'A' and resid 1831 through 1833' Processing helix chain 'A' and resid 1857 through 1860 No H-bonds generated for 'chain 'A' and resid 1857 through 1860' Processing helix chain 'A' and resid 1977 through 1980 No H-bonds generated for 'chain 'A' and resid 1977 through 1980' Processing helix chain 'A' and resid 1988 through 1994 Processing helix chain 'A' and resid 2072 through 2074 No H-bonds generated for 'chain 'A' and resid 2072 through 2074' Processing helix chain 'A' and resid 2085 through 2105 removed outlier: 3.635A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2135 Processing helix chain 'A' and resid 2148 through 2160 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2187 through 2189 No H-bonds generated for 'chain 'A' and resid 2187 through 2189' Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 127 through 135 Proline residue: B 134 - end of helix Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.667A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 296 Processing helix chain 'F' and resid 300 through 307 removed outlier: 3.646A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 321 removed outlier: 4.071A pdb=" N LYS F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 138 through 140 removed outlier: 3.642A pdb=" N MET A 180 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 246 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 220 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS A 244 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 222 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY A 242 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN A 224 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 240 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 754 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 830 " --> pdb=" O ASN A1528 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A1743 " --> pdb=" O ALA A1677 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A1679 " --> pdb=" O ARG A1741 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A1741 " --> pdb=" O TYR A1679 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A1681 " --> pdb=" O SER A1739 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER A1739 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN A1683 " --> pdb=" O ARG A1737 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG A1737 " --> pdb=" O GLN A1683 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN A1685 " --> pdb=" O ILE A1735 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A1735 " --> pdb=" O ASN A1685 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA A1687 " --> pdb=" O THR A1733 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR A1733 " --> pdb=" O ALA A1687 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN A1689 " --> pdb=" O PHE A1731 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE A1731 " --> pdb=" O ASN A1689 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A1691 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A1729 " --> pdb=" O ALA A1691 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A1728 " --> pdb=" O GLY A1771 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU A2258 " --> pdb=" O LYS A2198 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A2200 " --> pdb=" O ASP A2256 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP A2256 " --> pdb=" O PHE A2200 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A2202 " --> pdb=" O ARG A2254 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG A2254 " --> pdb=" O LEU A2202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A2253 " --> pdb=" O ILE A2269 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A2322 " --> pdb=" O ASP A2360 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A2348 " --> pdb=" O THR A2334 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A2336 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU A2346 " --> pdb=" O VAL A2336 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A2379 " --> pdb=" O ASN A2351 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 270 Processing sheet with id= C, first strand: chain 'A' and resid 275 through 282 Processing sheet with id= D, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.784A pdb=" N TYR A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 425 through 428 removed outlier: 6.120A pdb=" N LEU A 503 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU A 347 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 505 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 11.777A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 465 through 468 Processing sheet with id= G, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= H, first strand: chain 'A' and resid 527 through 529 Processing sheet with id= I, first strand: chain 'A' and resid 717 through 720 Processing sheet with id= J, first strand: chain 'A' and resid 770 through 773 Processing sheet with id= K, first strand: chain 'A' and resid 866 through 869 removed outlier: 3.611A pdb=" N ASP A1194 " --> pdb=" O GLN A1215 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A1217 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE A1192 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1250 through 1254 removed outlier: 3.624A pdb=" N LYS A 907 " --> pdb=" O TYR A 965 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 987 through 993 Processing sheet with id= N, first strand: chain 'A' and resid 1283 through 1291 Processing sheet with id= O, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id= P, first strand: chain 'A' and resid 1342 through 1348 Processing sheet with id= Q, first strand: chain 'A' and resid 1423 through 1426 removed outlier: 6.379A pdb=" N LEU A1510 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR A 857 " --> pdb=" O LEU A1510 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 1739 through 1742 Processing sheet with id= S, first strand: chain 'A' and resid 1848 through 1853 Processing sheet with id= T, first strand: chain 'A' and resid 2035 through 2042 removed outlier: 3.959A pdb=" N ALA A2208 " --> pdb=" O THR A2069 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 2044 through 2047 Processing sheet with id= V, first strand: chain 'A' and resid 2215 through 2217 Processing sheet with id= W, first strand: chain 'A' and resid 1945 through 1949 removed outlier: 6.655A pdb=" N ASN A2020 " --> pdb=" O LYS A1946 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A1948 " --> pdb=" O THR A2018 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N THR A2018 " --> pdb=" O VAL A1948 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= Y, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.321A pdb=" N GLU B 141 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 90 through 98 removed outlier: 6.471A pdb=" N LEU F 387 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 118 through 120 removed outlier: 4.180A pdb=" N ARG F 131 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 1041 through 1045 Processing sheet with id= AC, first strand: chain 'D' and resid 1106 through 1112 removed outlier: 6.384A pdb=" N ASP D1066 " --> pdb=" O LEU D1071 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU D1071 " --> pdb=" O ASP D1066 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.22 Time building geometry restraints manager: 8.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7248 1.34 - 1.46: 4951 1.46 - 1.58: 10083 1.58 - 1.70: 6 1.70 - 1.82: 92 Bond restraints: 22380 Sorted by residual: bond pdb=" C1 LMN A2501 " pdb=" O5 LMN A2501 " ideal model delta sigma weight residual 1.403 1.565 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sigma weight residual 1.409 1.507 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" CCF LMN A2501 " pdb=" OBX LMN A2501 " ideal model delta sigma weight residual 1.410 1.501 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" CCS LMN A2501 " pdb=" OBZ LMN A2501 " ideal model delta sigma weight residual 1.394 1.484 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " ideal model delta sigma weight residual 1.393 1.474 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 22375 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.54: 395 105.54 - 112.67: 11224 112.67 - 119.80: 7556 119.80 - 126.92: 11025 126.92 - 134.05: 180 Bond angle restraints: 30380 Sorted by residual: angle pdb=" CA PRO F 126 " pdb=" N PRO F 126 " pdb=" CD PRO F 126 " ideal model delta sigma weight residual 112.00 98.87 13.13 1.40e+00 5.10e-01 8.80e+01 angle pdb=" C ILE A2141 " pdb=" N GLY A2142 " pdb=" CA GLY A2142 " ideal model delta sigma weight residual 122.78 113.42 9.36 2.61e+00 1.47e-01 1.29e+01 angle pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " pdb=" CCR LMN A2501 " ideal model delta sigma weight residual 120.22 109.70 10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CA LYS F 294 " pdb=" CB LYS F 294 " pdb=" CG LYS F 294 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 angle pdb=" C PHE A 883 " pdb=" N ILE A 884 " pdb=" CA ILE A 884 " ideal model delta sigma weight residual 122.63 118.55 4.08 1.19e+00 7.06e-01 1.18e+01 ... (remaining 30375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 12263 24.53 - 49.06: 928 49.06 - 73.59: 155 73.59 - 98.12: 52 98.12 - 122.64: 15 Dihedral angle restraints: 13413 sinusoidal: 5391 harmonic: 8022 Sorted by residual: dihedral pdb=" CA ASP A1258 " pdb=" C ASP A1258 " pdb=" N LEU A1259 " pdb=" CA LEU A1259 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA PRO A1063 " pdb=" C PRO A1063 " pdb=" N LEU A1064 " pdb=" CA LEU A1064 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA THR F 169 " pdb=" C THR F 169 " pdb=" N GLU F 170 " pdb=" CA GLU F 170 " ideal model delta harmonic sigma weight residual 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 13410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2397 0.047 - 0.093: 650 0.093 - 0.139: 240 0.139 - 0.186: 18 0.186 - 0.232: 2 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CB ILE B 100 " pdb=" CA ILE B 100 " pdb=" CG1 ILE B 100 " pdb=" CG2 ILE B 100 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO F 126 " pdb=" N PRO F 126 " pdb=" C PRO F 126 " pdb=" CB PRO F 126 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB ILE A 344 " pdb=" CA ILE A 344 " pdb=" CG1 ILE A 344 " pdb=" CG2 ILE A 344 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 3304 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 125 " 0.070 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO F 126 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO F 126 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 126 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1651 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO A1652 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A1652 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1652 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 605 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 606 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.026 5.00e-02 4.00e+02 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 306 2.65 - 3.21: 19241 3.21 - 3.77: 35185 3.77 - 4.34: 51734 4.34 - 4.90: 82945 Nonbonded interactions: 189411 Sorted by model distance: nonbonded pdb=" OE1 GLN A 865 " pdb=" OH TYR A1006 " model vdw 2.082 2.440 nonbonded pdb=" NH1 ARG A2398 " pdb=" OD1 ASN A2400 " model vdw 2.095 2.520 nonbonded pdb=" ND2 ASN A1392 " pdb=" O GLY A1476 " model vdw 2.097 2.520 nonbonded pdb=" OH TYR A2115 " pdb=" O ILE A2141 " model vdw 2.113 2.440 nonbonded pdb=" OD1 ASN A 492 " pdb=" OG SER A 494 " model vdw 2.135 2.440 ... (remaining 189406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.090 Check model and map are aligned: 0.330 Set scattering table: 0.230 Process input model: 63.480 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 0.162 22380 Z= 0.336 Angle : 0.664 13.129 30380 Z= 0.362 Chirality : 0.048 0.232 3307 Planarity : 0.005 0.098 4022 Dihedral : 18.340 122.645 8293 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 2.00 % Allowed : 18.10 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.08 (0.16), residues: 2743 helix: -0.92 (0.29), residues: 303 sheet: 0.72 (0.16), residues: 1065 loop : -0.41 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1996 HIS 0.004 0.001 HIS A 291 PHE 0.022 0.002 PHE A1009 TYR 0.028 0.002 TYR D1042 ARG 0.006 0.001 ARG A2398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 243 time to evaluate : 2.752 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 28 residues processed: 282 average time/residue: 1.2959 time to fit residues: 419.7520 Evaluate side-chains 222 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1868 THR Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1040 SER Chi-restraints excluded: chain D residue 1079 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 501 GLN ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1387 ASN A1683 GLN A2012 ASN A2044 GLN ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 ASN B 143 GLN B 155 ASN D1053 ASN D1074 ASN D1084 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22380 Z= 0.389 Angle : 0.640 8.604 30380 Z= 0.339 Chirality : 0.050 0.368 3307 Planarity : 0.004 0.056 4022 Dihedral : 9.711 93.103 3182 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.64 % Rotamer: Outliers : 3.87 % Allowed : 16.52 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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 (0.16), residues: 2743 helix: -0.69 (0.31), residues: 285 sheet: 0.62 (0.16), residues: 1047 loop : -0.41 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1580 HIS 0.005 0.001 HIS A1653 PHE 0.026 0.002 PHE A1009 TYR 0.021 0.002 TYR A1104 ARG 0.006 0.000 ARG A1643 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 211 time to evaluate : 2.845 Fit side-chains revert: symmetry clash REVERT: A 1197 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: A 1722 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.5979 (p90) REVERT: A 2191 LYS cc_start: 0.3578 (OUTLIER) cc_final: 0.2847 (pttm) outliers start: 93 outliers final: 40 residues processed: 283 average time/residue: 1.3396 time to fit residues: 437.4935 Evaluate side-chains 233 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1849 ASP Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2191 LYS Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2364 SER Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 199 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN A 361 ASN ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 ASN A1683 GLN A1781 ASN A1880 ASN A1891 ASN ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2390 ASN B 143 GLN B 155 ASN F 353 GLN D1053 ASN D1074 ASN D1084 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22380 Z= 0.249 Angle : 0.580 8.244 30380 Z= 0.306 Chirality : 0.048 0.408 3307 Planarity : 0.004 0.052 4022 Dihedral : 8.589 83.518 3164 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 3.66 % Allowed : 16.77 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.17 (0.16), residues: 2743 helix: -0.63 (0.32), residues: 277 sheet: 0.55 (0.16), residues: 1047 loop : -0.44 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.023 0.001 PHE A1009 TYR 0.017 0.001 TYR A2159 ARG 0.008 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 205 time to evaluate : 2.546 Fit side-chains revert: symmetry clash REVERT: A 1020 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: A 1580 TRP cc_start: 0.7755 (OUTLIER) cc_final: 0.6433 (p-90) REVERT: A 1722 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6034 (p90) REVERT: A 1851 MET cc_start: 0.7790 (ttp) cc_final: 0.7578 (ttp) REVERT: A 2026 ASP cc_start: 0.6523 (OUTLIER) cc_final: 0.6304 (p0) REVERT: B 136 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.7950 (pp) outliers start: 88 outliers final: 37 residues processed: 269 average time/residue: 1.2884 time to fit residues: 400.2015 Evaluate side-chains 239 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1880 ASN Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 167 optimal weight: 0.0060 chunk 250 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 237 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 overall best weight: 1.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1338 GLN A1528 ASN ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 GLN A2020 ASN ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2390 ASN B 143 GLN B 155 ASN D1053 ASN D1074 ASN D1084 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22380 Z= 0.303 Angle : 0.588 8.698 30380 Z= 0.312 Chirality : 0.048 0.333 3307 Planarity : 0.004 0.053 4022 Dihedral : 8.229 86.697 3158 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 3.54 % Allowed : 16.73 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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 (0.16), residues: 2743 helix: -0.65 (0.32), residues: 279 sheet: 0.50 (0.16), residues: 1045 loop : -0.45 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.023 0.002 PHE A1009 TYR 0.020 0.001 TYR F 244 ARG 0.007 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 200 time to evaluate : 2.503 Fit side-chains revert: symmetry clash REVERT: A 884 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7073 (tp) REVERT: A 1197 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: A 1580 TRP cc_start: 0.7825 (OUTLIER) cc_final: 0.6533 (p-90) REVERT: A 1722 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6094 (p90) REVERT: A 2026 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6327 (p0) REVERT: A 2191 LYS cc_start: 0.3480 (OUTLIER) cc_final: 0.2914 (pttm) REVERT: B 136 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.7958 (pp) outliers start: 85 outliers final: 43 residues processed: 266 average time/residue: 1.3742 time to fit residues: 421.5364 Evaluate side-chains 243 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 193 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2191 LYS Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2364 SER Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 226 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 ASN A1683 GLN A1880 ASN A2020 ASN ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2390 ASN B 143 GLN B 155 ASN F 353 GLN D1053 ASN D1084 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22380 Z= 0.239 Angle : 0.564 9.531 30380 Z= 0.298 Chirality : 0.047 0.292 3307 Planarity : 0.004 0.052 4022 Dihedral : 7.812 82.199 3158 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 3.25 % Allowed : 16.94 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.23 (0.16), residues: 2743 helix: -0.61 (0.32), residues: 272 sheet: 0.45 (0.16), residues: 1047 loop : -0.45 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.023 0.001 PHE A1009 TYR 0.016 0.001 TYR A2159 ARG 0.008 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 202 time to evaluate : 3.556 Fit side-chains revert: symmetry clash REVERT: A 884 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6816 (tp) REVERT: A 1197 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: A 1580 TRP cc_start: 0.7781 (OUTLIER) cc_final: 0.6422 (p-90) REVERT: A 1722 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6153 (p90) REVERT: A 2026 ASP cc_start: 0.6521 (OUTLIER) cc_final: 0.6300 (p0) REVERT: A 2103 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: A 2191 LYS cc_start: 0.3416 (OUTLIER) cc_final: 0.2883 (pttm) REVERT: B 136 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.7966 (pp) outliers start: 78 outliers final: 42 residues processed: 258 average time/residue: 1.3723 time to fit residues: 409.2094 Evaluate side-chains 248 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 198 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 2022 ASP Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2191 LYS Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2364 SER Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain D residue 1102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 0.5980 chunk 238 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 ASN A1683 GLN ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 ASN A2390 ASN B 143 GLN B 155 ASN D1053 ASN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 22380 Z= 0.458 Angle : 0.650 10.295 30380 Z= 0.345 Chirality : 0.050 0.287 3307 Planarity : 0.004 0.053 4022 Dihedral : 7.831 81.617 3157 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.65 % Favored : 94.28 % Rotamer: Outliers : 3.45 % Allowed : 16.94 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.29 (0.16), residues: 2743 helix: -0.74 (0.32), residues: 280 sheet: 0.48 (0.16), residues: 1032 loop : -0.52 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1580 HIS 0.006 0.001 HIS A1672 PHE 0.025 0.002 PHE A1480 TYR 0.023 0.002 TYR A1104 ARG 0.010 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 195 time to evaluate : 2.593 Fit side-chains REVERT: A 884 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.6993 (tp) REVERT: A 1197 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: A 1580 TRP cc_start: 0.7946 (OUTLIER) cc_final: 0.6590 (p-90) REVERT: A 1722 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6428 (p90) REVERT: A 2026 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.6377 (p0) REVERT: A 2191 LYS cc_start: 0.3638 (OUTLIER) cc_final: 0.3396 (pttm) REVERT: B 136 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.7945 (pp) outliers start: 83 outliers final: 49 residues processed: 255 average time/residue: 1.3320 time to fit residues: 389.9604 Evaluate side-chains 236 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 180 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1733 THR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1942 LEU Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2191 LYS Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2364 SER Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 148 optimal weight: 0.3980 chunk 264 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 GLN ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22380 Z= 0.270 Angle : 0.587 9.941 30380 Z= 0.310 Chirality : 0.047 0.279 3307 Planarity : 0.004 0.055 4022 Dihedral : 7.368 82.571 3157 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 17.39 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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 (0.16), residues: 2743 helix: -0.67 (0.32), residues: 279 sheet: 0.40 (0.16), residues: 1047 loop : -0.49 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.024 0.001 PHE A1009 TYR 0.017 0.001 TYR A1104 ARG 0.009 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 194 time to evaluate : 2.636 Fit side-chains REVERT: A 188 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: A 884 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6782 (tp) REVERT: A 1197 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: A 1580 TRP cc_start: 0.7873 (OUTLIER) cc_final: 0.6445 (p-90) REVERT: A 1722 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6361 (p90) REVERT: A 2191 LYS cc_start: 0.3584 (OUTLIER) cc_final: 0.3318 (pttm) REVERT: B 136 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.7924 (pp) outliers start: 69 outliers final: 40 residues processed: 246 average time/residue: 1.4115 time to fit residues: 399.0662 Evaluate side-chains 238 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2191 LYS Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2364 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 207 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 GLN ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2390 ASN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22380 Z= 0.239 Angle : 0.571 10.283 30380 Z= 0.302 Chirality : 0.047 0.276 3307 Planarity : 0.004 0.054 4022 Dihedral : 6.906 82.100 3157 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.71 % Rotamer: Outliers : 2.62 % Allowed : 17.69 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.28 (0.16), residues: 2743 helix: -0.65 (0.32), residues: 272 sheet: 0.40 (0.16), residues: 1047 loop : -0.47 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.023 0.001 PHE A1009 TYR 0.022 0.001 TYR F 244 ARG 0.010 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 195 time to evaluate : 2.917 Fit side-chains REVERT: A 188 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6882 (tm-30) REVERT: A 747 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8282 (m-40) REVERT: A 836 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: A 884 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6615 (tp) REVERT: A 1197 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: A 1580 TRP cc_start: 0.7846 (OUTLIER) cc_final: 0.6431 (p-90) REVERT: A 1722 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6420 (p90) REVERT: A 2026 ASP cc_start: 0.6506 (OUTLIER) cc_final: 0.6292 (p0) REVERT: A 2191 LYS cc_start: 0.3720 (OUTLIER) cc_final: 0.3447 (pttm) REVERT: B 136 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7933 (pp) outliers start: 63 outliers final: 40 residues processed: 242 average time/residue: 1.3646 time to fit residues: 381.1162 Evaluate side-chains 241 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 191 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2191 LYS Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2364 SER Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 246 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 ASN A1583 ASN A1683 GLN A2020 ASN ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2390 ASN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22380 Z= 0.205 Angle : 0.553 9.990 30380 Z= 0.293 Chirality : 0.046 0.276 3307 Planarity : 0.004 0.054 4022 Dihedral : 6.600 81.507 3157 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 2.54 % Allowed : 17.85 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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 (0.16), residues: 2743 helix: -0.61 (0.32), residues: 272 sheet: 0.41 (0.16), residues: 1048 loop : -0.45 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.023 0.001 PHE A1009 TYR 0.018 0.001 TYR B 55 ARG 0.010 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 205 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: A 836 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6857 (tt0) REVERT: A 862 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.5556 (mp0) REVERT: A 884 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6522 (tp) REVERT: A 1580 TRP cc_start: 0.7778 (OUTLIER) cc_final: 0.6377 (p-90) REVERT: A 1722 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6355 (p90) REVERT: A 2191 LYS cc_start: 0.3604 (OUTLIER) cc_final: 0.3329 (pttm) REVERT: B 136 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7998 (pp) outliers start: 61 outliers final: 38 residues processed: 250 average time/residue: 1.3284 time to fit residues: 382.4307 Evaluate side-chains 244 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 198 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2191 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2364 SER Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 167 optimal weight: 0.0020 chunk 133 optimal weight: 10.0000 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 GLN ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2390 ASN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22380 Z= 0.339 Angle : 0.601 10.821 30380 Z= 0.319 Chirality : 0.048 0.280 3307 Planarity : 0.004 0.054 4022 Dihedral : 6.648 81.500 3153 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 2.50 % Allowed : 18.19 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.28 (0.16), residues: 2743 helix: -0.67 (0.32), residues: 280 sheet: 0.40 (0.16), residues: 1047 loop : -0.46 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.024 0.002 PHE A1009 TYR 0.020 0.002 TYR B 55 ARG 0.010 0.000 ARG A 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 189 time to evaluate : 2.657 Fit side-chains REVERT: A 188 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: A 836 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6897 (tt0) REVERT: A 884 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6678 (tp) REVERT: A 1197 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: A 1580 TRP cc_start: 0.7849 (OUTLIER) cc_final: 0.6508 (p-90) REVERT: A 1722 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6426 (p90) REVERT: A 2026 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6407 (p0) REVERT: A 2191 LYS cc_start: 0.3748 (OUTLIER) cc_final: 0.3436 (pttm) REVERT: B 136 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8002 (pp) outliers start: 60 outliers final: 42 residues processed: 233 average time/residue: 1.3973 time to fit residues: 375.4173 Evaluate side-chains 240 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 189 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1727 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1942 LEU Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2191 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2364 SER Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 122 GLN Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 GLN A1880 ASN ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2390 ASN B 143 GLN B 155 ASN D1053 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.094017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.071717 restraints weight = 34024.278| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.15 r_work: 0.2822 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22380 Z= 0.335 Angle : 0.607 10.260 30380 Z= 0.322 Chirality : 0.048 0.281 3307 Planarity : 0.004 0.054 4022 Dihedral : 6.690 81.770 3153 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.71 % Rotamer: Outliers : 2.54 % Allowed : 18.31 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.29 (0.16), residues: 2743 helix: -0.67 (0.32), residues: 279 sheet: 0.40 (0.16), residues: 1044 loop : -0.48 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.024 0.002 PHE A1009 TYR 0.020 0.002 TYR B 55 ARG 0.015 0.001 ARG A 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7784.05 seconds wall clock time: 139 minutes 43.11 seconds (8383.11 seconds total)