Starting phenix.real_space_refine on Fri Dec 8 23:40:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk5_14755/12_2023/7zk5_14755.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk5_14755/12_2023/7zk5_14755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk5_14755/12_2023/7zk5_14755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk5_14755/12_2023/7zk5_14755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk5_14755/12_2023/7zk5_14755.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk5_14755/12_2023/7zk5_14755.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 6067 2.51 5 N 1566 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 802": "OD1" <-> "OD2" Residue "A ASP 882": "OD1" <-> "OD2" Residue "A TYR 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1140": "OE1" <-> "OE2" Residue "A ASP 1167": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9435 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 9435 Unusual residues: {' MG': 2, 'ATP': 2, 'JIZ': 1, 'Y01': 5} Classifications: {'peptide': 1177, 'undetermined': 10, 'water': 33} Link IDs: {'PTRANS': 29, 'TRANS': 1147, None: 43} Not linked: pdbres="ALA A1271 " pdbres="ATP A2001 " Not linked: pdbres="ATP A2001 " pdbres=" MG A2002 " Not linked: pdbres=" MG A2002 " pdbres="ATP A2003 " Not linked: pdbres="ATP A2003 " pdbres=" MG A2004 " Not linked: pdbres=" MG A2004 " pdbres="Y01 A2005 " ... (remaining 38 not shown) Chain breaks: 1 Time building chain proxies: 5.48, per 1000 atoms: 0.58 Number of scatterers: 9435 At special positions: 0 Unit cell: (72.819, 84.537, 149.823, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1758 8.00 N 1566 7.00 C 6067 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 70.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.714A pdb=" N THR A 37 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET A 38 " --> pdb=" O VAL A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 38' Processing helix chain 'A' and resid 42 through 71 removed outlier: 3.940A pdb=" N ASP A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 3.602A pdb=" N MET A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 152 removed outlier: 3.622A pdb=" N TRP A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 180 removed outlier: 5.013A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 206 removed outlier: 3.710A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 216 through 256 removed outlier: 4.559A pdb=" N VAL A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 265 through 319 removed outlier: 3.716A pdb=" N ASN A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 344 removed outlier: 3.651A pdb=" N ILE A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 367 removed outlier: 4.016A pdb=" N TYR A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 458 through 465 removed outlier: 3.500A pdb=" N ILE A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.982A pdb=" N THR A 518 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 542 Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 586 through 590 removed outlier: 3.672A pdb=" N ASN A 590 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 703 through 737 removed outlier: 3.597A pdb=" N PHE A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 4.701A pdb=" N SER A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 749 through 795 Processing helix chain 'A' and resid 796 through 801 removed outlier: 3.506A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 823 Processing helix chain 'A' and resid 826 through 850 removed outlier: 3.806A pdb=" N ILE A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 899 removed outlier: 3.549A pdb=" N LEU A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 4.160A pdb=" N ALA A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN A 878 " --> pdb=" O MET A 874 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 880 " --> pdb=" O SER A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 907 Processing helix chain 'A' and resid 908 through 920 Processing helix chain 'A' and resid 920 through 962 removed outlier: 3.625A pdb=" N HIS A 932 " --> pdb=" O MET A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 990 Processing helix chain 'A' and resid 990 through 1010 removed outlier: 3.785A pdb=" N ARG A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.664A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1108 removed outlier: 3.530A pdb=" N GLN A1108 " --> pdb=" O TRP A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1157 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 4.129A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1217 Processing helix chain 'A' and resid 1229 through 1234 Processing helix chain 'A' and resid 1252 through 1259 removed outlier: 3.582A pdb=" N GLN A1259 " --> pdb=" O GLN A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1271 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413 removed outlier: 6.887A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N PHE A 390 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER A 448 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASN A 392 " --> pdb=" O MET A 446 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N MET A 446 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.324A pdb=" N GLY A 467 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP A 551 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 469 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 548 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE A 581 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 550 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL A 419 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A 604 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP A 598 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1049 through 1056 removed outlier: 6.946A pdb=" N GLN A1050 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A1037 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU A1052 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A1036 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A1087 " --> pdb=" O VAL A1036 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.230A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE A1226 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A1062 " --> pdb=" O VAL A1225 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A1249 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN A1243 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL A1247 " --> pdb=" O GLN A1243 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1519 1.29 - 1.42: 2380 1.42 - 1.55: 5596 1.55 - 1.68: 31 1.68 - 1.82: 64 Bond restraints: 9590 Sorted by residual: bond pdb=" C03 JIZ A2010 " pdb=" N02 JIZ A2010 " ideal model delta sigma weight residual 1.367 1.639 -0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C08 JIZ A2010 " pdb=" N04 JIZ A2010 " ideal model delta sigma weight residual 1.366 1.617 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C13 JIZ A2010 " pdb=" N06 JIZ A2010 " ideal model delta sigma weight residual 1.366 1.616 -0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C02 JIZ A2010 " pdb=" S01 JIZ A2010 " ideal model delta sigma weight residual 1.728 1.546 0.182 2.00e-02 2.50e+03 8.28e+01 bond pdb=" C03 JIZ A2010 " pdb=" C04 JIZ A2010 " ideal model delta sigma weight residual 1.360 1.518 -0.158 2.00e-02 2.50e+03 6.27e+01 ... (remaining 9585 not shown) Histogram of bond angle deviations from ideal: 98.36 - 106.66: 265 106.66 - 114.96: 5795 114.96 - 123.25: 6484 123.25 - 131.55: 447 131.55 - 139.85: 18 Bond angle restraints: 13009 Sorted by residual: angle pdb=" N ALA A 94 " pdb=" CA ALA A 94 " pdb=" C ALA A 94 " ideal model delta sigma weight residual 112.72 102.26 10.46 1.28e+00 6.10e-01 6.68e+01 angle pdb=" C THR A 807 " pdb=" CA THR A 807 " pdb=" CB THR A 807 " ideal model delta sigma weight residual 110.96 121.57 -10.61 1.54e+00 4.22e-01 4.75e+01 angle pdb=" N ASP A 95 " pdb=" CA ASP A 95 " pdb=" C ASP A 95 " ideal model delta sigma weight residual 111.36 104.11 7.25 1.09e+00 8.42e-01 4.42e+01 angle pdb=" C ARG A 258 " pdb=" N THR A 259 " pdb=" CA THR A 259 " ideal model delta sigma weight residual 120.44 128.56 -8.12 1.30e+00 5.92e-01 3.90e+01 angle pdb=" C VAL A1165 " pdb=" N GLY A1166 " pdb=" CA GLY A1166 " ideal model delta sigma weight residual 122.83 115.41 7.42 1.21e+00 6.83e-01 3.76e+01 ... (remaining 13004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5432 17.96 - 35.92: 439 35.92 - 53.88: 94 53.88 - 71.84: 21 71.84 - 89.80: 10 Dihedral angle restraints: 5996 sinusoidal: 2625 harmonic: 3371 Sorted by residual: dihedral pdb=" C ILE A 897 " pdb=" N ILE A 897 " pdb=" CA ILE A 897 " pdb=" CB ILE A 897 " ideal model delta harmonic sigma weight residual -122.00 -136.83 14.83 0 2.50e+00 1.60e-01 3.52e+01 dihedral pdb=" C THR A 807 " pdb=" N THR A 807 " pdb=" CA THR A 807 " pdb=" CB THR A 807 " ideal model delta harmonic sigma weight residual -122.00 -136.80 14.80 0 2.50e+00 1.60e-01 3.50e+01 dihedral pdb=" C PHE A 728 " pdb=" N PHE A 728 " pdb=" CA PHE A 728 " pdb=" CB PHE A 728 " ideal model delta harmonic sigma weight residual -122.60 -109.87 -12.73 0 2.50e+00 1.60e-01 2.59e+01 ... (remaining 5993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1355 0.099 - 0.198: 111 0.198 - 0.296: 20 0.296 - 0.395: 8 0.395 - 0.494: 3 Chirality restraints: 1497 Sorted by residual: chirality pdb=" CA THR A 807 " pdb=" N THR A 807 " pdb=" C THR A 807 " pdb=" CB THR A 807 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA ILE A 897 " pdb=" N ILE A 897 " pdb=" C ILE A 897 " pdb=" CB ILE A 897 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA THR A 811 " pdb=" N THR A 811 " pdb=" C THR A 811 " pdb=" CB THR A 811 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 1494 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 320 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C LYS A 320 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS A 320 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU A 321 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 314 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C THR A 314 " -0.070 2.00e-02 2.50e+03 pdb=" O THR A 314 " 0.026 2.00e-02 2.50e+03 pdb=" N SER A 315 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1118 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C LEU A1118 " 0.063 2.00e-02 2.50e+03 pdb=" O LEU A1118 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A1119 " -0.022 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 104 2.63 - 3.20: 8844 3.20 - 3.76: 15414 3.76 - 4.33: 21981 4.33 - 4.90: 34638 Nonbonded interactions: 80981 Sorted by model distance: nonbonded pdb=" OG SER A1073 " pdb="MG MG A2004 " model vdw 2.061 2.170 nonbonded pdb="MG MG A2004 " pdb=" O HOH A2104 " model vdw 2.078 2.170 nonbonded pdb="MG MG A2004 " pdb=" O HOH A2109 " model vdw 2.079 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2107 " model vdw 2.079 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2111 " model vdw 2.088 2.170 ... (remaining 80976 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.170 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.040 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.010 0.272 9590 Z= 0.695 Angle : 1.030 17.652 13009 Z= 0.673 Chirality : 0.065 0.494 1497 Planarity : 0.006 0.068 1617 Dihedral : 14.219 89.804 3836 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.78 % Rotamer: Outliers : 0.10 % Allowed : 1.76 % Favored : 98.14 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1173 helix: 1.23 (0.18), residues: 787 sheet: 0.75 (0.62), residues: 70 loop : -0.21 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 208 HIS 0.006 0.001 HIS A1003 PHE 0.027 0.002 PHE A 331 TYR 0.022 0.002 TYR A 322 ARG 0.009 0.001 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.105 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 1.4079 time to fit residues: 307.6765 Evaluate side-chains 135 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 458 ASN A 749 ASN ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 969 ASN A1050 GLN ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9590 Z= 0.182 Angle : 0.533 7.275 13009 Z= 0.279 Chirality : 0.040 0.158 1497 Planarity : 0.004 0.060 1617 Dihedral : 9.066 71.137 1718 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.97 % Allowed : 10.77 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1173 helix: 1.72 (0.18), residues: 790 sheet: 0.75 (0.60), residues: 70 loop : -0.22 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 208 HIS 0.006 0.001 HIS A1003 PHE 0.021 0.002 PHE A 508 TYR 0.013 0.001 TYR A 113 ARG 0.004 0.000 ARG A1164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.045 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 3 residues processed: 147 average time/residue: 1.3670 time to fit residues: 214.2937 Evaluate side-chains 125 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.7074 time to fit residues: 3.1853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 119 optimal weight: 50.0000 chunk 98 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 GLN A 749 ASN A 820 GLN ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 986 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9590 Z= 0.209 Angle : 0.512 8.490 13009 Z= 0.268 Chirality : 0.040 0.137 1497 Planarity : 0.004 0.057 1617 Dihedral : 8.978 71.339 1718 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.07 % Allowed : 12.22 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.24), residues: 1173 helix: 1.92 (0.18), residues: 787 sheet: 0.95 (0.60), residues: 70 loop : -0.32 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 208 HIS 0.006 0.001 HIS A1003 PHE 0.021 0.002 PHE A 767 TYR 0.017 0.001 TYR A 949 ARG 0.004 0.000 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.115 Fit side-chains outliers start: 20 outliers final: 5 residues processed: 139 average time/residue: 1.3695 time to fit residues: 203.4752 Evaluate side-chains 122 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.9993 time to fit residues: 3.5639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN A 820 GLN ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 GLN ** A1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9590 Z= 0.244 Angle : 0.533 9.040 13009 Z= 0.274 Chirality : 0.041 0.143 1497 Planarity : 0.004 0.053 1617 Dihedral : 9.013 74.716 1718 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.45 % Allowed : 13.35 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1173 helix: 1.90 (0.18), residues: 787 sheet: 1.03 (0.59), residues: 70 loop : -0.37 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 208 HIS 0.007 0.001 HIS A 60 PHE 0.020 0.002 PHE A 767 TYR 0.016 0.002 TYR A 949 ARG 0.004 0.000 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.036 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 134 average time/residue: 1.2654 time to fit residues: 182.0288 Evaluate side-chains 125 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.7042 time to fit residues: 3.2450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN A 820 GLN ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9590 Z= 0.254 Angle : 0.529 9.552 13009 Z= 0.275 Chirality : 0.041 0.139 1497 Planarity : 0.004 0.048 1617 Dihedral : 9.115 77.004 1718 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.07 % Allowed : 13.15 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.24), residues: 1173 helix: 1.88 (0.18), residues: 789 sheet: 1.15 (0.59), residues: 70 loop : -0.35 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 208 HIS 0.006 0.001 HIS A 60 PHE 0.029 0.002 PHE A 940 TYR 0.014 0.002 TYR A 113 ARG 0.004 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.084 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 139 average time/residue: 1.3193 time to fit residues: 197.0124 Evaluate side-chains 126 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.9006 time to fit residues: 3.3767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 749 ASN A 820 GLN ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 986 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9590 Z= 0.175 Angle : 0.493 8.181 13009 Z= 0.255 Chirality : 0.039 0.137 1497 Planarity : 0.003 0.043 1617 Dihedral : 8.919 73.128 1718 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.48 % Allowed : 13.35 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.24), residues: 1173 helix: 2.05 (0.18), residues: 789 sheet: 1.17 (0.60), residues: 70 loop : -0.36 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 208 HIS 0.005 0.001 HIS A1003 PHE 0.018 0.001 PHE A 508 TYR 0.018 0.001 TYR A 949 ARG 0.004 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.009 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 142 average time/residue: 1.3054 time to fit residues: 198.3089 Evaluate side-chains 128 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.8051 time to fit residues: 3.3121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 749 ASN A 820 GLN ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 986 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9590 Z= 0.229 Angle : 0.522 9.189 13009 Z= 0.271 Chirality : 0.040 0.158 1497 Planarity : 0.003 0.043 1617 Dihedral : 9.060 75.850 1718 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.86 % Allowed : 14.29 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.24), residues: 1173 helix: 1.94 (0.18), residues: 791 sheet: 1.14 (0.60), residues: 70 loop : -0.35 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 132 HIS 0.005 0.001 HIS A 60 PHE 0.028 0.002 PHE A 940 TYR 0.019 0.002 TYR A 949 ARG 0.005 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.960 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 1.3271 time to fit residues: 199.5441 Evaluate side-chains 129 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 2.2057 time to fit residues: 3.8418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 GLN ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 986 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9590 Z= 0.209 Angle : 0.517 9.223 13009 Z= 0.267 Chirality : 0.040 0.134 1497 Planarity : 0.003 0.040 1617 Dihedral : 9.036 75.120 1718 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.97 % Allowed : 14.70 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.24), residues: 1173 helix: 1.98 (0.18), residues: 791 sheet: 1.11 (0.59), residues: 70 loop : -0.37 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1104 HIS 0.005 0.001 HIS A1003 PHE 0.019 0.002 PHE A 508 TYR 0.022 0.001 TYR A 949 ARG 0.005 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.031 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 134 average time/residue: 1.3039 time to fit residues: 187.5572 Evaluate side-chains 127 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.2348 time to fit residues: 1.7744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 GLN ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 986 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9590 Z= 0.181 Angle : 0.507 9.593 13009 Z= 0.261 Chirality : 0.039 0.181 1497 Planarity : 0.003 0.039 1617 Dihedral : 8.935 73.080 1718 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.55 % Allowed : 15.42 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.24), residues: 1173 helix: 2.06 (0.18), residues: 785 sheet: 1.16 (0.60), residues: 70 loop : -0.40 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 208 HIS 0.005 0.001 HIS A1003 PHE 0.027 0.002 PHE A 940 TYR 0.020 0.001 TYR A 949 ARG 0.005 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.098 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 137 average time/residue: 1.2879 time to fit residues: 189.3963 Evaluate side-chains 122 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.8873 time to fit residues: 3.4022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 50.0000 chunk 111 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.0270 chunk 76 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 overall best weight: 1.8444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 GLN A 835 ASN A 878 GLN A 986 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9590 Z= 0.311 Angle : 0.590 15.461 13009 Z= 0.301 Chirality : 0.043 0.258 1497 Planarity : 0.004 0.040 1617 Dihedral : 9.249 79.366 1718 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.45 % Allowed : 15.63 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1173 helix: 1.82 (0.18), residues: 784 sheet: 1.20 (0.60), residues: 70 loop : -0.43 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A1104 HIS 0.006 0.001 HIS A 60 PHE 0.023 0.002 PHE A 619 TYR 0.023 0.002 TYR A 949 ARG 0.006 0.000 ARG A 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.040 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 128 average time/residue: 1.3124 time to fit residues: 180.0219 Evaluate side-chains 120 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.4677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A 986 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.157413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115805 restraints weight = 9955.726| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.79 r_work: 0.3185 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9590 Z= 0.235 Angle : 0.542 13.634 13009 Z= 0.279 Chirality : 0.041 0.164 1497 Planarity : 0.003 0.039 1617 Dihedral : 9.155 77.399 1718 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.04 % Allowed : 15.73 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.24), residues: 1173 helix: 1.87 (0.18), residues: 786 sheet: 1.17 (0.60), residues: 70 loop : -0.42 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 158 HIS 0.005 0.001 HIS A 60 PHE 0.020 0.002 PHE A 508 TYR 0.024 0.002 TYR A 949 ARG 0.005 0.000 ARG A 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.47 seconds wall clock time: 69 minutes 22.40 seconds (4162.40 seconds total)