Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 19:27:28 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/12_2021/6dmb_7963_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/12_2021/6dmb_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_7963/12_2021/6dmb_7963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/12_2021/6dmb_7963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/12_2021/6dmb_7963_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmb_7963/12_2021/6dmb_7963_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 7945 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7945 Unusual residues: {'Y01': 2, 'NAG': 7} Classifications: {'undetermined': 9, 'peptide': 990} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 42, 'TRANS': 946, None: 9, 'PCIS': 1} Not linked: pdbres="SER A1185 " pdbres="NAG A1801 " Not linked: pdbres="NAG A1801 " pdbres="NAG A1802 " Not linked: pdbres="NAG A1802 " pdbres="NAG A1803 " Not linked: pdbres="NAG A1803 " pdbres="NAG A1804 " Not linked: pdbres="NAG A1804 " pdbres="NAG A1805 " ... (remaining 4 not shown) Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 14 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 Time building chain proxies: 4.96, per 1000 atoms: 0.62 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 Amimo 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 A1805 " - " NAG A1806 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1805 " - " ASN A1000 " " NAG A1807 " - " ASN A 141 " Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.1 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... running ksdssp... Secondary structure from input PDB file: 40 helices and 2 sheets defined 52.5% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 3.693A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 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) removed outlier: 3.516A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 128 No H-bonds generated for 'chain 'A' and resid 125 through 128' Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 389 through 408 removed outlier: 3.657A pdb=" N GLU A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 440 through 456 removed outlier: 3.661A pdb=" N LEU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 490 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 499 through 505 Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 507 through 525 removed outlier: 4.104A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 563 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 568 through 604 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) Processing helix chain 'A' and resid 732 through 744 removed outlier: 3.713A pdb=" N LYS A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Proline residue: A 742 - end of helix Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 751 through 769 Processing helix chain 'A' and resid 786 through 797 Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.654A pdb=" N TYR A 820 " --> pdb=" O GLN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 Processing helix chain 'A' and resid 878 through 887 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) Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 920 through 929 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 931 through 936 Processing helix chain 'A' and resid 985 through 1003 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) Processing helix chain 'A' and resid 1013 through 1021 removed outlier: 5.534A pdb=" N GLN A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR A1021 " --> pdb=" O PHE A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1046 removed outlier: 3.510A pdb=" N PHE A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1074 Processing helix chain 'A' and resid 1081 through 1105 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 1113 through 1121 removed outlier: 3.525A pdb=" N ALA A1118 " --> pdb=" O ARG A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1137 Processing helix chain 'A' and resid 1147 through 1154 Processing helix chain 'A' and resid 1156 through 1177 Proline residue: A1172 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 360 through 363 Processing sheet with id= B, 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) 334 hydrogen bonds defined for protein. 996 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: 2.22 Time building geometry restraints manager: 3.45 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: 4549 24.57 - 49.14: 206 49.14 - 73.71: 17 73.71 - 98.28: 3 98.28 - 122.85: 1 Dihedral angle restraints: 4776 sinusoidal: 1890 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 4773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1083 0.091 - 0.182: 189 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: 1944 2.79 - 3.32: 7528 3.32 - 3.85: 12942 3.85 - 4.37: 14096 4.37 - 4.90: 23624 Nonbonded interactions: 60134 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 60129 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 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. 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 Write .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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.110 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 23.900 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.310 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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= 0.564 Angle : 1.354 15.028 11085 Z= 0.689 Chirality : 0.068 0.454 1289 Planarity : 0.009 0.095 1374 Dihedral : 13.320 122.852 2911 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 % 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 *********************** 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 : 0.983 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 outliers start: 16 outliers final: 4 residues processed: 226 average time/residue: 0.1867 time to fit residues: 57.8253 Evaluate side-chains 111 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.936 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0699 time to fit residues: 1.6999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 872 ASN A 889 GLN A 929 ASN A1099 HIS A1112 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8142 Z= 0.243 Angle : 0.823 11.820 11085 Z= 0.403 Chirality : 0.044 0.276 1289 Planarity : 0.006 0.080 1374 Dihedral : 8.502 111.251 1137 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.51 % Allowed : 12.17 % Favored : 87.32 % Rotamer Outliers : 5.95 % 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: -3.03 (0.25), residues: 986 helix: -0.77 (0.21), residues: 552 sheet: -2.52 (0.68), residues: 51 loop : -3.87 (0.27), residues: 383 *********************** 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 175 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 27 residues processed: 161 average time/residue: 0.1614 time to fit residues: 37.7415 Evaluate side-chains 124 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0782 time to fit residues: 5.0452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.0570 chunk 80 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8142 Z= 0.182 Angle : 0.778 9.828 11085 Z= 0.369 Chirality : 0.043 0.363 1289 Planarity : 0.006 0.075 1374 Dihedral : 7.827 112.589 1137 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.05 % Favored : 88.64 % Rotamer Outliers : 3.76 % 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: -2.22 (0.26), residues: 986 helix: -0.05 (0.22), residues: 551 sheet: -1.78 (0.78), residues: 51 loop : -3.67 (0.28), residues: 384 *********************** 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 165 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 10 residues processed: 153 average time/residue: 0.1694 time to fit residues: 37.5271 Evaluate side-chains 124 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0773 time to fit residues: 2.6467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 0.3980 chunk 46 optimal weight: 0.2980 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 A 576 GLN ** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8142 Z= 0.180 Angle : 0.756 9.977 11085 Z= 0.358 Chirality : 0.044 0.526 1289 Planarity : 0.005 0.071 1374 Dihedral : 7.604 112.914 1137 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.97 % Favored : 87.93 % Rotamer Outliers : 2.55 % 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: -1.84 (0.27), residues: 986 helix: 0.29 (0.22), residues: 552 sheet: -1.53 (0.80), residues: 51 loop : -3.59 (0.29), residues: 383 *********************** 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 147 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 139 average time/residue: 0.1654 time to fit residues: 33.1818 Evaluate side-chains 118 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0754 time to fit residues: 2.3026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 24 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4334 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= 0.171 Angle : 0.753 11.445 11085 Z= 0.353 Chirality : 0.042 0.238 1289 Planarity : 0.005 0.069 1374 Dihedral : 7.316 113.420 1137 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.26 % Favored : 88.64 % Rotamer Outliers : 2.55 % 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: -1.56 (0.27), residues: 986 helix: 0.51 (0.23), residues: 555 sheet: -1.55 (0.78), residues: 51 loop : -3.46 (0.29), residues: 380 *********************** 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 142 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 134 average time/residue: 0.1771 time to fit residues: 34.1677 Evaluate side-chains 119 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0834 time to fit residues: 2.7883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 31 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 802 ASN ** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 8142 Z= 0.196 Angle : 0.749 11.752 11085 Z= 0.354 Chirality : 0.041 0.223 1289 Planarity : 0.006 0.097 1374 Dihedral : 7.211 113.683 1137 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.26 % Favored : 88.54 % Rotamer Outliers : 1.21 % 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: -1.22 (0.28), residues: 986 helix: 0.82 (0.23), residues: 555 sheet: -1.72 (0.76), residues: 51 loop : -3.31 (0.30), residues: 380 *********************** 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 129 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 123 average time/residue: 0.1764 time to fit residues: 31.6319 Evaluate side-chains 108 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0829 time to fit residues: 2.1853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.0050 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 A 872 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 8142 Z= 0.171 Angle : 0.785 21.217 11085 Z= 0.357 Chirality : 0.041 0.214 1289 Planarity : 0.008 0.210 1374 Dihedral : 7.115 114.063 1137 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.65 % Favored : 89.25 % Rotamer Outliers : 1.58 % 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: -1.09 (0.28), residues: 986 helix: 0.96 (0.23), residues: 552 sheet: -1.80 (0.74), residues: 52 loop : -3.26 (0.30), residues: 382 *********************** 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 121 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 115 average time/residue: 0.1801 time to fit residues: 29.8682 Evaluate side-chains 114 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0874 time to fit residues: 2.6735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 8142 Z= 0.239 Angle : 0.784 14.693 11085 Z= 0.367 Chirality : 0.042 0.219 1289 Planarity : 0.007 0.179 1374 Dihedral : 7.241 113.936 1137 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.87 % Favored : 88.03 % Rotamer Outliers : 1.33 % 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: -0.90 (0.28), residues: 986 helix: 1.18 (0.23), residues: 550 sheet: -1.87 (0.73), residues: 52 loop : -3.22 (0.30), residues: 384 *********************** 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 111 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.986 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 108 average time/residue: 0.1741 time to fit residues: 27.4992 Evaluate side-chains 99 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0777 time to fit residues: 1.7587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 HIS ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4780 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= 0.204 Angle : 0.777 13.520 11085 Z= 0.360 Chirality : 0.042 0.213 1289 Planarity : 0.007 0.170 1374 Dihedral : 7.174 113.780 1137 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer Outliers : 0.97 % 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: -0.86 (0.28), residues: 986 helix: 1.21 (0.24), residues: 546 sheet: -1.76 (0.74), residues: 52 loop : -3.17 (0.30), residues: 388 *********************** 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 108 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.004 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 104 average time/residue: 0.1755 time to fit residues: 26.7629 Evaluate side-chains 100 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0880 time to fit residues: 2.0982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 0.0870 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: 7.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 8142 Z= 0.186 Angle : 0.788 13.737 11085 Z= 0.360 Chirality : 0.041 0.201 1289 Planarity : 0.007 0.161 1374 Dihedral : 7.041 113.787 1137 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer Outliers : 0.49 % 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: -0.83 (0.28), residues: 986 helix: 1.21 (0.23), residues: 544 sheet: -1.71 (0.76), residues: 52 loop : -3.11 (0.30), residues: 390 ********************** 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 114 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 111 average time/residue: 0.1737 time to fit residues: 28.1247 Evaluate side-chains 103 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0969 time to fit residues: 1.7960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 HIS A1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093059 restraints weight = 20455.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095833 restraints weight = 12135.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096684 restraints weight = 7860.239| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 8142 Z= 0.317 Angle : 0.835 13.588 11085 Z= 0.394 Chirality : 0.045 0.236 1289 Planarity : 0.007 0.163 1374 Dihedral : 7.395 113.142 1137 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer Outliers : 1.09 % 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: -0.90 (0.28), residues: 986 helix: 1.17 (0.23), residues: 539 sheet: -1.82 (0.76), residues: 52 loop : -3.11 (0.31), residues: 395 =============================================================================== Job complete usr+sys time: 1574.83 seconds wall clock time: 29 minutes 28.15 seconds (1768.15 seconds total)