Starting phenix.real_space_refine on Wed Feb 14 05:28:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/02_2024/6dmb_7963.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/02_2024/6dmb_7963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/02_2024/6dmb_7963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/02_2024/6dmb_7963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/02_2024/6dmb_7963.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/02_2024/6dmb_7963.pdb" } resolution = 3.9 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 768 atoms to isotropic. 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 42 5.16 5 C 5189 2.51 5 N 1290 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ARG 906": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1113": "NH1" <-> "NH2" Residue "A ARG 1114": "NH1" <-> "NH2" Residue "A ARG 1150": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7945 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7777 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 946} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Unusual residues: {'NAG': 5, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.74, per 1000 atoms: 0.60 Number of scatterers: 7945 At special positions: 0 Unit cell: (94.917, 77.461, 141.83, 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 42 16.00 O 1424 8.00 N 1290 7.00 C 5189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG B 1 " - " ASN A1000 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 60.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 74 through 96 removed outlier: 4.175A pdb=" N TRP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.807A pdb=" N PHE A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.649A pdb=" N TRP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.685A pdb=" N ASP A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 234' Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.534A pdb=" N ASN A 258 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 259 " --> pdb=" O TRP A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 260 through 271 removed outlier: 4.069A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 removed outlier: 3.751A pdb=" N ALA A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.790A pdb=" N ILE A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 411 removed outlier: 3.657A pdb=" N GLU A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 439 through 457 removed outlier: 3.661A pdb=" N LEU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 491 removed outlier: 3.842A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 506 through 526 removed outlier: 3.688A pdb=" N VAL A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 564 removed outlier: 3.890A pdb=" N THR A 544 " --> pdb=" O CYS A 540 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 605 removed outlier: 4.022A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.147A pdb=" N SER A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP A 605 " --> pdb=" O TYR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.713A pdb=" N LYS A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 745 removed outlier: 3.619A pdb=" N LEU A 745 " --> pdb=" O PRO A 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 745' Processing helix chain 'A' and resid 746 through 749 Processing helix chain 'A' and resid 750 through 770 removed outlier: 4.205A pdb=" N ILE A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 Processing helix chain 'A' and resid 815 through 828 removed outlier: 3.654A pdb=" N TYR A 820 " --> pdb=" O GLN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 863 removed outlier: 3.688A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 888 removed outlier: 3.707A pdb=" N VAL A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 882 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 903 Processing helix chain 'A' and resid 919 through 930 removed outlier: 3.565A pdb=" N LEU A 923 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 925 " --> pdb=" O ILE A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 937 removed outlier: 3.861A pdb=" N SER A 937 " --> pdb=" O ALA A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1004 removed outlier: 3.760A pdb=" N ILE A 997 " --> pdb=" O LYS A 993 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A1003 " --> pdb=" O SER A 999 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 Processing helix chain 'A' and resid 1019 through 1022 Processing helix chain 'A' and resid 1026 through 1046 removed outlier: 3.510A pdb=" N PHE A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1075 removed outlier: 3.796A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1106 removed outlier: 3.556A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1122 removed outlier: 3.525A pdb=" N ALA A1118 " --> pdb=" O ARG A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1138 Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1155 through 1178 Proline residue: A1172 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 363 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 331 removed outlier: 4.751A pdb=" N SER A 331 " --> pdb=" O MET A 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 removed outlier: 7.242A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 975 through 978 removed outlier: 3.738A pdb=" N TYR A 804 " --> pdb=" O ASN A1011 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1134 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: 2.17 Time building geometry restraints manager: 3.32 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: 2419 1.34 - 1.46: 1964 1.46 - 1.59: 3690 1.59 - 1.71: 0 1.71 - 1.83: 69 Bond restraints: 8142 Sorted by residual: bond pdb=" CAY Y01 A1809 " pdb=" OAW Y01 A1809 " ideal model delta sigma weight residual 1.332 1.462 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" CAY Y01 A1808 " pdb=" OAW Y01 A1808 " ideal model delta sigma weight residual 1.332 1.452 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C ASP A 293 " pdb=" N ARG A 294 " ideal model delta sigma weight residual 1.331 1.252 0.079 1.59e-02 3.96e+03 2.47e+01 bond pdb=" CAX Y01 A1808 " pdb=" OAH Y01 A1808 " ideal model delta sigma weight residual 1.248 1.328 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" CAX Y01 A1809 " pdb=" OAH Y01 A1809 " ideal model delta sigma weight residual 1.248 1.328 -0.080 2.00e-02 2.50e+03 1.60e+01 ... (remaining 8137 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.21: 177 105.21 - 112.44: 4039 112.44 - 119.66: 2968 119.66 - 126.89: 3770 126.89 - 134.11: 131 Bond angle restraints: 11085 Sorted by residual: angle pdb=" C LEU A 458 " pdb=" N ARG A 459 " pdb=" CA ARG A 459 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" N VAL A 908 " pdb=" CA VAL A 908 " pdb=" C VAL A 908 " ideal model delta sigma weight residual 113.53 108.53 5.00 9.80e-01 1.04e+00 2.60e+01 angle pdb=" C GLU A 836 " pdb=" N ASN A 837 " pdb=" CA ASN A 837 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C LEU A1048 " pdb=" N ASN A1049 " pdb=" CA ASN A1049 " ideal model delta sigma weight residual 121.80 133.18 -11.38 2.44e+00 1.68e-01 2.18e+01 angle pdb=" N GLU A 947 " pdb=" CA GLU A 947 " pdb=" C GLU A 947 " ideal model delta sigma weight residual 110.91 116.30 -5.39 1.17e+00 7.31e-01 2.12e+01 ... (remaining 11080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.57: 4738 24.57 - 49.14: 227 49.14 - 73.71: 23 73.71 - 98.28: 6 98.28 - 122.85: 3 Dihedral angle restraints: 4997 sinusoidal: 2111 harmonic: 2886 Sorted by residual: dihedral pdb=" CA ASN A1049 " pdb=" C ASN A1049 " pdb=" N PRO A1050 " pdb=" CA PRO A1050 " ideal model delta harmonic sigma weight residual 180.00 -120.68 -59.32 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA LYS A 867 " pdb=" C LYS A 867 " pdb=" N ILE A 868 " pdb=" CA ILE A 868 " ideal model delta harmonic sigma weight residual -180.00 -132.90 -47.10 0 5.00e+00 4.00e-02 8.87e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 166.11 -73.11 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 4994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1079 0.091 - 0.182: 193 0.182 - 0.273: 14 0.273 - 0.363: 2 0.363 - 0.454: 1 Chirality restraints: 1289 Sorted by residual: chirality pdb=" C1 NAG A1804 " pdb=" ND2 ASN A 875 " pdb=" C2 NAG A1804 " pdb=" O5 NAG A1804 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CB ILE A 531 " pdb=" CA ILE A 531 " pdb=" CG1 ILE A 531 " pdb=" CG2 ILE A 531 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG A1801 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG A1801 " pdb=" O5 NAG A1801 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1286 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 869 " -0.063 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO A 870 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 870 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 870 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 812 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 813 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 813 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 813 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1081 " 0.051 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO A1082 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A1082 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1082 " 0.043 5.00e-02 4.00e+02 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1940 2.79 - 3.32: 7486 3.32 - 3.85: 12883 3.85 - 4.37: 13993 4.37 - 4.90: 23612 Nonbonded interactions: 59914 Sorted by model distance: nonbonded pdb=" O MET A 956 " pdb=" OG1 THR A 959 " model vdw 2.266 2.440 nonbonded pdb=" O GLY A 774 " pdb=" OH TYR A1021 " model vdw 2.275 2.440 nonbonded pdb=" O CYS A 998 " pdb=" OG1 THR A1002 " model vdw 2.295 2.440 nonbonded pdb=" O TYR A 452 " pdb=" OG1 THR A 456 " model vdw 2.317 2.440 nonbonded pdb=" O ASN A 120 " pdb=" OG SER A 494 " model vdw 2.338 2.440 ... (remaining 59909 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 2.820 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.050 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 0.009 0.130 8142 Z= 0.572 Angle : 1.362 15.028 11085 Z= 0.690 Chirality : 0.068 0.454 1289 Planarity : 0.009 0.095 1374 Dihedral : 13.898 122.852 3132 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.18 % Favored : 86.21 % Rotamer: Outliers : 1.94 % Allowed : 8.74 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 4.65 % Twisted General : 0.63 % 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: -4.55 (0.21), residues: 986 helix: -2.31 (0.17), residues: 525 sheet: -3.36 (0.56), residues: 52 loop : -3.90 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 337 HIS 0.011 0.002 HIS A 520 PHE 0.045 0.004 PHE A1015 TYR 0.032 0.003 TYR A 222 ARG 0.008 0.001 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TRP cc_start: 0.7803 (m100) cc_final: 0.7107 (m-10) REVERT: A 183 LEU cc_start: 0.9037 (tp) cc_final: 0.8744 (tt) REVERT: A 374 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 416 THR cc_start: 0.8533 (p) cc_final: 0.8249 (t) REVERT: A 455 LEU cc_start: 0.8678 (mm) cc_final: 0.8429 (tt) REVERT: A 490 LEU cc_start: 0.8894 (mm) cc_final: 0.8401 (tt) REVERT: A 550 LEU cc_start: 0.9214 (tp) cc_final: 0.8872 (tp) REVERT: A 598 MET cc_start: 0.8044 (mmm) cc_final: 0.7783 (tmm) REVERT: A 988 VAL cc_start: 0.9322 (t) cc_final: 0.8278 (m) REVERT: A 1029 LEU cc_start: 0.8798 (tt) cc_final: 0.8478 (mm) REVERT: A 1076 ILE cc_start: 0.9051 (mm) cc_final: 0.8837 (mm) REVERT: A 1128 ASP cc_start: 0.7284 (m-30) cc_final: 0.6996 (m-30) REVERT: A 1146 ASP cc_start: 0.7669 (t0) cc_final: 0.7237 (t0) REVERT: A 1165 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8641 (mt) outliers start: 16 outliers final: 4 residues processed: 226 average time/residue: 0.1875 time to fit residues: 57.5959 Evaluate side-chains 117 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1165 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 95 GLN A 178 HIS A 324 ASN A 375 HIS ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 802 ASN A 828 ASN A 846 HIS A 853 GLN A 856 GLN A 889 GLN A 929 ASN A1099 HIS A1112 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8142 Z= 0.191 Angle : 0.814 10.572 11085 Z= 0.395 Chirality : 0.043 0.226 1289 Planarity : 0.006 0.080 1374 Dihedral : 9.059 59.456 1368 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.87 % Favored : 87.83 % Rotamer: Outliers : 5.70 % Allowed : 15.66 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % 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: -2.82 (0.25), residues: 986 helix: -0.69 (0.21), residues: 564 sheet: -2.51 (0.71), residues: 46 loop : -3.67 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 236 HIS 0.005 0.001 HIS A 817 PHE 0.031 0.002 PHE A 800 TYR 0.021 0.001 TYR A 740 ARG 0.003 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TRP cc_start: 0.7615 (m100) cc_final: 0.6976 (m-10) REVERT: A 281 MET cc_start: 0.8667 (ttp) cc_final: 0.8310 (ptp) REVERT: A 332 ARG cc_start: 0.8087 (mtt90) cc_final: 0.7855 (mpt-90) REVERT: A 374 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 416 THR cc_start: 0.8382 (p) cc_final: 0.8141 (t) REVERT: A 432 LYS cc_start: 0.9068 (tmtt) cc_final: 0.8663 (tmtt) REVERT: A 455 LEU cc_start: 0.8350 (mm) cc_final: 0.8111 (tt) REVERT: A 490 LEU cc_start: 0.8648 (mm) cc_final: 0.8196 (tt) REVERT: A 988 VAL cc_start: 0.9272 (t) cc_final: 0.9070 (p) outliers start: 47 outliers final: 21 residues processed: 180 average time/residue: 0.1645 time to fit residues: 41.9313 Evaluate side-chains 129 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 950 HIS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 74 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8142 Z= 0.185 Angle : 0.812 10.889 11085 Z= 0.383 Chirality : 0.047 0.747 1289 Planarity : 0.006 0.077 1374 Dihedral : 8.571 58.124 1364 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.95 % Favored : 88.84 % Rotamer: Outliers : 5.70 % Allowed : 17.84 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % 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: -1.96 (0.27), residues: 986 helix: -0.00 (0.22), residues: 576 sheet: -1.75 (0.78), residues: 51 loop : -3.47 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 78 HIS 0.004 0.001 HIS A 950 PHE 0.025 0.001 PHE A 800 TYR 0.023 0.001 TYR A 740 ARG 0.002 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 129 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.4876 (pmm) cc_final: 0.4652 (pmm) REVERT: A 281 MET cc_start: 0.8681 (ttp) cc_final: 0.8323 (ptp) REVERT: A 360 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8632 (pp) REVERT: A 374 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 416 THR cc_start: 0.8354 (p) cc_final: 0.8011 (t) REVERT: A 455 LEU cc_start: 0.8312 (mm) cc_final: 0.8078 (tt) REVERT: A 490 LEU cc_start: 0.8613 (mm) cc_final: 0.8146 (tt) REVERT: A 856 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7116 (tm-30) outliers start: 47 outliers final: 23 residues processed: 165 average time/residue: 0.1644 time to fit residues: 39.3808 Evaluate side-chains 142 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 856 GLN ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8142 Z= 0.253 Angle : 0.809 12.187 11085 Z= 0.383 Chirality : 0.045 0.292 1289 Planarity : 0.006 0.079 1374 Dihedral : 8.456 58.867 1364 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.37 % Favored : 87.53 % Rotamer: Outliers : 5.58 % Allowed : 21.12 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % 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: -1.64 (0.28), residues: 986 helix: 0.30 (0.22), residues: 579 sheet: -1.39 (0.83), residues: 51 loop : -3.48 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 78 HIS 0.005 0.001 HIS A 950 PHE 0.021 0.002 PHE A 800 TYR 0.020 0.001 TYR A 740 ARG 0.002 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.5128 (pmm) cc_final: 0.4822 (pmm) REVERT: A 198 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7063 (mtmp) REVERT: A 360 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8676 (pp) REVERT: A 374 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 416 THR cc_start: 0.8481 (p) cc_final: 0.8125 (t) REVERT: A 455 LEU cc_start: 0.8329 (mm) cc_final: 0.8052 (tt) REVERT: A 490 LEU cc_start: 0.8667 (mm) cc_final: 0.8168 (tt) REVERT: A 1076 ILE cc_start: 0.9152 (mm) cc_final: 0.8894 (mm) outliers start: 46 outliers final: 36 residues processed: 140 average time/residue: 0.1544 time to fit residues: 32.0152 Evaluate side-chains 140 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 102 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8142 Z= 0.188 Angle : 0.778 11.541 11085 Z= 0.361 Chirality : 0.042 0.271 1289 Planarity : 0.005 0.074 1374 Dihedral : 8.073 58.777 1364 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.36 % Favored : 88.54 % Rotamer: Outliers : 5.46 % Allowed : 21.00 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.11 % 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: -1.27 (0.28), residues: 986 helix: 0.66 (0.23), residues: 575 sheet: -1.25 (0.84), residues: 51 loop : -3.41 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 256 HIS 0.003 0.001 HIS A 950 PHE 0.020 0.001 PHE A 800 TYR 0.022 0.001 TYR A 740 ARG 0.001 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 118 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.4535 (pmm) cc_final: 0.4174 (pmm) REVERT: A 198 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7021 (mtmp) REVERT: A 360 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8650 (pp) REVERT: A 374 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7522 (mm-30) REVERT: A 416 THR cc_start: 0.8418 (p) cc_final: 0.8033 (t) REVERT: A 490 LEU cc_start: 0.8538 (mm) cc_final: 0.8115 (tt) REVERT: A 1048 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7252 (tp) REVERT: A 1076 ILE cc_start: 0.9165 (mm) cc_final: 0.8882 (mm) outliers start: 45 outliers final: 27 residues processed: 149 average time/residue: 0.1554 time to fit residues: 33.9266 Evaluate side-chains 134 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain A residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8142 Z= 0.227 Angle : 0.805 11.827 11085 Z= 0.372 Chirality : 0.043 0.183 1289 Planarity : 0.005 0.085 1374 Dihedral : 8.071 59.236 1364 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.47 % Favored : 87.42 % Rotamer: Outliers : 5.10 % Allowed : 21.36 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.28), residues: 986 helix: 0.87 (0.23), residues: 569 sheet: -1.33 (0.83), residues: 51 loop : -3.28 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 256 HIS 0.004 0.001 HIS A 520 PHE 0.022 0.001 PHE A 800 TYR 0.023 0.001 TYR A 740 ARG 0.003 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 105 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8252 (m-40) cc_final: 0.6993 (p0) REVERT: A 192 MET cc_start: 0.4923 (pmm) cc_final: 0.4416 (pmm) REVERT: A 198 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7137 (mtmp) REVERT: A 360 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8699 (pp) REVERT: A 374 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 416 THR cc_start: 0.8455 (p) cc_final: 0.8067 (t) REVERT: A 490 LEU cc_start: 0.8519 (mm) cc_final: 0.8074 (tt) REVERT: A 493 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.5961 (mm) REVERT: A 845 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8847 (tm) REVERT: A 905 GLN cc_start: 0.7223 (tp-100) cc_final: 0.7012 (tp40) REVERT: A 1048 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7392 (tt) REVERT: A 1076 ILE cc_start: 0.9183 (mm) cc_final: 0.8875 (mm) outliers start: 42 outliers final: 28 residues processed: 135 average time/residue: 0.1487 time to fit residues: 30.0661 Evaluate side-chains 132 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8142 Z= 0.178 Angle : 0.795 12.698 11085 Z= 0.361 Chirality : 0.042 0.196 1289 Planarity : 0.006 0.111 1374 Dihedral : 7.970 59.249 1364 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.66 % Favored : 88.24 % Rotamer: Outliers : 4.98 % Allowed : 21.48 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % 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: -0.84 (0.29), residues: 986 helix: 1.00 (0.23), residues: 574 sheet: -1.25 (0.83), residues: 51 loop : -3.17 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 256 HIS 0.004 0.001 HIS A 817 PHE 0.024 0.001 PHE A 800 TYR 0.024 0.001 TYR A 740 ARG 0.002 0.000 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 112 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8262 (m-40) cc_final: 0.7088 (p0) REVERT: A 192 MET cc_start: 0.4573 (pmm) cc_final: 0.4092 (pmm) REVERT: A 198 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7151 (mtmp) REVERT: A 360 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8639 (pp) REVERT: A 374 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7425 (mm-30) REVERT: A 434 PHE cc_start: 0.8272 (t80) cc_final: 0.7994 (t80) REVERT: A 490 LEU cc_start: 0.8369 (mm) cc_final: 0.7890 (tt) REVERT: A 773 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8229 (p0) REVERT: A 1076 ILE cc_start: 0.9198 (mm) cc_final: 0.8891 (mm) outliers start: 41 outliers final: 29 residues processed: 144 average time/residue: 0.1557 time to fit residues: 32.4842 Evaluate side-chains 132 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain A residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.0030 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 802 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8142 Z= 0.200 Angle : 0.790 13.593 11085 Z= 0.362 Chirality : 0.042 0.178 1289 Planarity : 0.006 0.101 1374 Dihedral : 7.811 59.562 1362 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.17 % Favored : 87.73 % Rotamer: Outliers : 4.85 % Allowed : 22.33 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % 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: -0.76 (0.29), residues: 986 helix: 1.10 (0.23), residues: 570 sheet: -1.39 (0.81), residues: 51 loop : -3.12 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 278 HIS 0.015 0.001 HIS A 739 PHE 0.023 0.001 PHE A 800 TYR 0.023 0.001 TYR A 740 ARG 0.002 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8263 (m-40) cc_final: 0.7079 (p0) REVERT: A 183 LEU cc_start: 0.8222 (tt) cc_final: 0.7918 (mt) REVERT: A 192 MET cc_start: 0.4803 (pmm) cc_final: 0.4386 (pmm) REVERT: A 198 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7188 (mtmp) REVERT: A 360 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8647 (pp) REVERT: A 374 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7402 (mm-30) REVERT: A 490 LEU cc_start: 0.8350 (mm) cc_final: 0.7914 (tt) REVERT: A 773 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8191 (p0) REVERT: A 845 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8813 (tm) REVERT: A 905 GLN cc_start: 0.7129 (tp-100) cc_final: 0.6871 (tp40) REVERT: A 1076 ILE cc_start: 0.9203 (mm) cc_final: 0.8886 (mm) outliers start: 40 outliers final: 31 residues processed: 128 average time/residue: 0.1653 time to fit residues: 31.3798 Evaluate side-chains 133 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain A residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 53 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8142 Z= 0.192 Angle : 0.789 13.820 11085 Z= 0.361 Chirality : 0.043 0.340 1289 Planarity : 0.005 0.092 1374 Dihedral : 7.607 57.646 1360 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 4.98 % Allowed : 22.33 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % 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: -0.61 (0.29), residues: 986 helix: 1.22 (0.23), residues: 564 sheet: -1.47 (0.80), residues: 51 loop : -2.97 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 256 HIS 0.017 0.001 HIS A 739 PHE 0.024 0.001 PHE A 800 TYR 0.023 0.001 TYR A 740 ARG 0.002 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 101 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8250 (m-40) cc_final: 0.7109 (p0) REVERT: A 183 LEU cc_start: 0.8165 (tt) cc_final: 0.7814 (mt) REVERT: A 192 MET cc_start: 0.4718 (pmm) cc_final: 0.4243 (pmm) REVERT: A 198 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7180 (mtmp) REVERT: A 281 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8788 (ptp) REVERT: A 360 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8639 (pp) REVERT: A 490 LEU cc_start: 0.8389 (mm) cc_final: 0.7958 (tt) REVERT: A 587 MET cc_start: 0.8614 (tmm) cc_final: 0.8366 (ppp) REVERT: A 773 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8181 (p0) REVERT: A 845 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8681 (tm) REVERT: A 1076 ILE cc_start: 0.9213 (mm) cc_final: 0.8901 (mm) outliers start: 41 outliers final: 31 residues processed: 128 average time/residue: 0.1550 time to fit residues: 29.1196 Evaluate side-chains 132 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain A residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.0040 chunk 24 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 889 GLN ** A 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8142 Z= 0.174 Angle : 0.772 13.456 11085 Z= 0.351 Chirality : 0.041 0.223 1289 Planarity : 0.005 0.088 1374 Dihedral : 7.386 59.613 1360 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 3.88 % Allowed : 23.18 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.11 % 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: -0.50 (0.29), residues: 986 helix: 1.30 (0.23), residues: 562 sheet: -1.41 (0.80), residues: 51 loop : -2.88 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 256 HIS 0.017 0.001 HIS A 739 PHE 0.026 0.001 PHE A 800 TYR 0.022 0.001 TYR A 740 ARG 0.001 0.000 ARG A 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8296 (m-40) cc_final: 0.7311 (p0) REVERT: A 192 MET cc_start: 0.4542 (pmm) cc_final: 0.4051 (pmm) REVERT: A 198 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7094 (mtmp) REVERT: A 281 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8641 (ptp) REVERT: A 360 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8589 (pp) REVERT: A 490 LEU cc_start: 0.8305 (mm) cc_final: 0.7931 (tt) REVERT: A 587 MET cc_start: 0.8623 (tmm) cc_final: 0.8377 (ppp) REVERT: A 845 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8679 (tm) REVERT: A 1076 ILE cc_start: 0.9229 (mm) cc_final: 0.8872 (mm) outliers start: 32 outliers final: 25 residues processed: 130 average time/residue: 0.1627 time to fit residues: 31.0179 Evaluate side-chains 128 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain A residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.4980 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 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 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** A 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096952 restraints weight = 19524.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099627 restraints weight = 11083.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101406 restraints weight = 7490.169| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 8142 Z= 0.225 Angle : 0.806 16.332 11085 Z= 0.365 Chirality : 0.048 0.809 1289 Planarity : 0.006 0.127 1374 Dihedral : 7.511 59.771 1360 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 4.00 % Allowed : 24.03 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.29), residues: 986 helix: 1.33 (0.23), residues: 561 sheet: -1.37 (0.80), residues: 51 loop : -2.81 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 256 HIS 0.017 0.001 HIS A 739 PHE 0.024 0.001 PHE A 800 TYR 0.023 0.001 TYR A 740 ARG 0.001 0.000 ARG A 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1676.31 seconds wall clock time: 31 minutes 21.00 seconds (1881.00 seconds total)