Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 16:14:25 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/12_2021/6oeu_7795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/12_2021/6oeu_7795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/12_2021/6oeu_7795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/12_2021/6oeu_7795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/12_2021/6oeu_7795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/12_2021/6oeu_7795.pdb" } resolution = 3.5 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= 0.003 sd= 0.103 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 GLU 122": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A ARG 530": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ASP 605": "OD1" <-> "OD2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 772": "NH1" <-> "NH2" Residue "A ASP 779": "OD1" <-> "OD2" Residue "A TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 811": "OD1" <-> "OD2" Residue "A ASP 821": "OD1" <-> "OD2" Residue "A ARG 824": "NH1" <-> "NH2" Residue "A ASP 860": "OD1" <-> "OD2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 982": "NH1" <-> "NH2" Residue "A ASP 983": "OD1" <-> "OD2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1150": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 7310 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7310 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8, 'peptide': 964} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 39, 'TRANS': 924, None: 8} Not linked: pdbres="SER A1176 " pdbres="NAG A1501 " Not linked: pdbres="NAG A1501 " pdbres="NAG A1502 " Not linked: pdbres="NAG A1502 " pdbres="NAG A1503 " Not linked: pdbres="NAG A1503 " pdbres="NAG A1504 " Not linked: pdbres="NAG A1504 " pdbres="NAG A1505 " ... (remaining 3 not shown) Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 472 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 11, 'ASN:plan1': 8, 'TRP:plan': 5, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 267 Time building chain proxies: 4.41, per 1000 atoms: 0.60 Number of scatterers: 7310 At special positions: 0 Unit cell: (133, 83, 87, 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 34 16.00 O 1327 8.00 N 1215 7.00 C 4734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 A1501 " - " NAG A1502 " " NAG A1503 " - " NAG A1504 " " NAG A1505 " - " NAG A1506 " " NAG A1507 " - " NAG A1508 " NAG-ASN " NAG A1507 " - " ASN A1000 " Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.2 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 59.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 77 through 94 removed outlier: 4.616A pdb=" N LEU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.692A pdb=" N GLY A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 146 removed outlier: 4.015A pdb=" N ARG A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.991A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.676A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.834A pdb=" N ILE A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 342' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 409 removed outlier: 3.606A pdb=" N GLN A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 438 through 456 removed outlier: 3.603A pdb=" N VAL A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 502 through 525 removed outlier: 4.478A pdb=" N LEU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 517 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 561 removed outlier: 5.271A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 602 Proline residue: A 593 - end of helix removed outlier: 3.559A pdb=" N ARG A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 746 through 770 Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.660A pdb=" N ASP A 779 " --> pdb=" O ASP A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 removed outlier: 3.843A pdb=" N ASP A 789 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.980A pdb=" N ASN A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 838 " --> pdb=" O GLU A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 838' Processing helix chain 'A' and resid 843 through 866 removed outlier: 3.627A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'A' and resid 918 through 930 removed outlier: 3.674A pdb=" N SER A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 938 removed outlier: 3.595A pdb=" N TYR A 934 " --> pdb=" O ASP A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1004 removed outlier: 3.689A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 removed outlier: 3.549A pdb=" N TRP A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1048 removed outlier: 3.537A pdb=" N TRP A1027 " --> pdb=" O GLY A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1075 Processing helix chain 'A' and resid 1079 through 1102 removed outlier: 4.105A pdb=" N VAL A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY A1091 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1106 removed outlier: 3.685A pdb=" N THR A1106 " --> pdb=" O ALA A1103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1103 through 1106' Processing helix chain 'A' and resid 1112 through 1138 removed outlier: 3.574A pdb=" N VAL A1116 " --> pdb=" O ASN A1112 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Proline residue: A1125 - end of helix Processing helix chain 'A' and resid 1139 through 1142 Processing helix chain 'A' and resid 1147 through 1175 removed outlier: 5.149A pdb=" N LEU A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) Proline residue: A1172 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.674A pdb=" N ASN A 154 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 366 " --> pdb=" O ASN A 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA3, first strand: chain 'A' and resid 800 through 801 Processing sheet with id=AA4, first strand: chain 'A' and resid 972 through 975 407 hydrogen bonds defined for protein. 1191 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: 2.25 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1341 1.33 - 1.45: 1835 1.45 - 1.58: 4234 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 7466 Sorted by residual: bond pdb=" N ILE A 342 " pdb=" CA ILE A 342 " ideal model delta sigma weight residual 1.456 1.504 -0.048 9.50e-03 1.11e+04 2.51e+01 bond pdb=" N VAL A 275 " pdb=" CA VAL A 275 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.04e-02 9.25e+03 2.05e+01 bond pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta sigma weight residual 1.455 1.484 -0.029 7.00e-03 2.04e+04 1.69e+01 bond pdb=" N ILE A 963 " pdb=" CA ILE A 963 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.00e-03 1.23e+04 1.43e+01 bond pdb=" N GLY A 214 " pdb=" CA GLY A 214 " ideal model delta sigma weight residual 1.446 1.486 -0.040 1.06e-02 8.90e+03 1.39e+01 ... (remaining 7461 not shown) Histogram of bond angle deviations from ideal: 91.14 - 99.82: 4 99.82 - 108.50: 469 108.50 - 117.19: 4760 117.19 - 125.87: 4752 125.87 - 134.55: 187 Bond angle restraints: 10172 Sorted by residual: angle pdb=" N SER A 415 " pdb=" CA SER A 415 " pdb=" C SER A 415 " ideal model delta sigma weight residual 110.23 91.14 19.09 1.45e+00 4.76e-01 1.73e+02 angle pdb=" C2 NAG A1501 " pdb=" C1 NAG A1501 " pdb=" O5 NAG A1501 " ideal model delta sigma weight residual 109.64 116.12 -6.48 5.38e-01 3.45e+00 1.45e+02 angle pdb=" N LEU A 121 " pdb=" CA LEU A 121 " pdb=" C LEU A 121 " ideal model delta sigma weight residual 108.69 93.01 15.68 1.77e+00 3.19e-01 7.85e+01 angle pdb=" N THR A 416 " pdb=" CA THR A 416 " pdb=" C THR A 416 " ideal model delta sigma weight residual 112.45 101.16 11.29 1.39e+00 5.18e-01 6.60e+01 angle pdb=" C SER A 415 " pdb=" CA SER A 415 " pdb=" CB SER A 415 " ideal model delta sigma weight residual 109.72 122.46 -12.74 1.66e+00 3.63e-01 5.89e+01 ... (remaining 10167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.35: 3998 20.35 - 40.71: 313 40.71 - 61.06: 53 61.06 - 81.41: 6 81.41 - 101.77: 3 Dihedral angle restraints: 4373 sinusoidal: 1573 harmonic: 2800 Sorted by residual: dihedral pdb=" CA SER A 313 " pdb=" C SER A 313 " pdb=" N THR A 314 " pdb=" CA THR A 314 " ideal model delta harmonic sigma weight residual -180.00 -144.14 -35.86 0 5.00e+00 4.00e-02 5.14e+01 dihedral pdb=" C ALA A 246 " pdb=" N ALA A 246 " pdb=" CA ALA A 246 " pdb=" CB ALA A 246 " ideal model delta harmonic sigma weight residual -122.60 -106.73 -15.87 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" CA HIS A 201 " pdb=" C HIS A 201 " pdb=" N LEU A 202 " pdb=" CA LEU A 202 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 4370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.333: 1214 0.333 - 0.666: 2 0.666 - 0.999: 1 0.999 - 1.332: 0 1.332 - 1.665: 3 Chirality restraints: 1220 Sorted by residual: chirality pdb=" C1 NAG A1506 " pdb=" O4 NAG A1505 " pdb=" C2 NAG A1506 " pdb=" O5 NAG A1506 " both_signs ideal model delta sigma weight residual False -2.40 -0.73 -1.67 2.00e-02 2.50e+03 6.93e+03 chirality pdb=" C1 NAG A1508 " pdb=" O4 NAG A1507 " pdb=" C2 NAG A1508 " pdb=" O5 NAG A1508 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-02 2.50e+03 5.18e+03 chirality pdb=" C1 NAG A1504 " pdb=" O4 NAG A1503 " pdb=" C2 NAG A1504 " pdb=" O5 NAG A1504 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-02 2.50e+03 4.53e+03 ... (remaining 1217 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1000 " -0.263 2.00e-02 2.50e+03 2.50e-01 7.83e+02 pdb=" CG ASN A1000 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN A1000 " 0.080 2.00e-02 2.50e+03 pdb=" ND2 ASN A1000 " 0.389 2.00e-02 2.50e+03 pdb=" C1 NAG A1507 " -0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 229 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ILE A 229 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE A 229 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A 230 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 156 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C GLN A 156 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN A 156 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 157 " 0.018 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 168 2.71 - 3.25: 7011 3.25 - 3.80: 11318 3.80 - 4.35: 14002 4.35 - 4.90: 23666 Nonbonded interactions: 56165 Sorted by model distance: nonbonded pdb=" ND2 ASN A 141 " pdb=" C1 NAG A1501 " model vdw 2.157 3.550 nonbonded pdb=" ND2 ASN A 414 " pdb=" O5 NAG A1505 " model vdw 2.322 2.520 nonbonded pdb=" ND2 ASN A 414 " pdb=" C2 NAG A1505 " model vdw 2.396 3.550 nonbonded pdb=" O GLY A1129 " pdb=" OG SER A1132 " model vdw 2.397 2.440 nonbonded pdb=" O SER A 799 " pdb=" OG SER A 799 " model vdw 2.399 2.440 ... (remaining 56160 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 34 5.16 5 C 4734 2.51 5 N 1215 2.21 5 O 1327 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: 0.750 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: 4.050 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 22.900 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 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 : 0.014 0.062 7466 Z= 0.942 Angle : 1.887 19.090 10172 Z= 1.421 Chirality : 0.111 1.665 1220 Planarity : 0.005 0.037 1278 Dihedral : 14.999 101.767 2565 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.33 % Favored : 89.56 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.81 (0.22), residues: 958 helix: -1.66 (0.18), residues: 542 sheet: -2.05 (0.71), residues: 43 loop : -3.88 (0.26), residues: 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 180 average time/residue: 0.1928 time to fit residues: 46.3486 Evaluate side-chains 116 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0682 time to fit residues: 1.2963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 312 ASN A 414 ASN A 527 GLN A1166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 7466 Z= 0.230 Angle : 0.715 11.683 10172 Z= 0.366 Chirality : 0.043 0.287 1220 Planarity : 0.005 0.085 1278 Dihedral : 7.601 104.530 1073 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.26), residues: 958 helix: -0.37 (0.21), residues: 561 sheet: -1.63 (0.75), residues: 43 loop : -3.24 (0.30), residues: 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.808 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 142 average time/residue: 0.1609 time to fit residues: 32.7649 Evaluate side-chains 119 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0710 time to fit residues: 2.4667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7466 Z= 0.190 Angle : 0.609 10.584 10172 Z= 0.316 Chirality : 0.041 0.342 1220 Planarity : 0.005 0.081 1278 Dihedral : 7.221 103.987 1073 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.27), residues: 958 helix: 0.23 (0.22), residues: 559 sheet: -1.30 (0.75), residues: 43 loop : -3.02 (0.30), residues: 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.821 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 128 average time/residue: 0.1525 time to fit residues: 28.4478 Evaluate side-chains 115 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0761 time to fit residues: 1.5621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 177 GLN A 361 GLN A 520 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7466 Z= 0.169 Angle : 0.591 9.285 10172 Z= 0.302 Chirality : 0.041 0.329 1220 Planarity : 0.005 0.087 1278 Dihedral : 7.004 103.980 1073 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 958 helix: 0.53 (0.22), residues: 562 sheet: -0.89 (0.78), residues: 45 loop : -2.81 (0.31), residues: 351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 0.817 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 134 average time/residue: 0.1528 time to fit residues: 30.3839 Evaluate side-chains 119 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0765 time to fit residues: 3.0526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 chunk 80 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 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 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7466 Z= 0.175 Angle : 0.578 8.528 10172 Z= 0.295 Chirality : 0.040 0.337 1220 Planarity : 0.005 0.088 1278 Dihedral : 6.880 103.577 1073 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.27), residues: 958 helix: 0.64 (0.22), residues: 568 sheet: -0.70 (0.78), residues: 45 loop : -2.75 (0.32), residues: 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.862 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 123 average time/residue: 0.1535 time to fit residues: 27.8391 Evaluate side-chains 112 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0818 time to fit residues: 1.9788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A 929 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7466 Z= 0.253 Angle : 0.630 8.865 10172 Z= 0.318 Chirality : 0.043 0.383 1220 Planarity : 0.005 0.086 1278 Dihedral : 6.930 102.792 1073 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.27), residues: 958 helix: 0.51 (0.22), residues: 564 sheet: -0.46 (0.77), residues: 45 loop : -2.81 (0.31), residues: 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.839 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 121 average time/residue: 0.1676 time to fit residues: 29.1699 Evaluate side-chains 118 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0750 time to fit residues: 2.4512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 0.0370 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7466 Z= 0.169 Angle : 0.602 12.077 10172 Z= 0.303 Chirality : 0.041 0.341 1220 Planarity : 0.006 0.087 1278 Dihedral : 6.835 103.775 1073 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.27), residues: 958 helix: 0.69 (0.22), residues: 568 sheet: -0.32 (0.76), residues: 43 loop : -2.80 (0.31), residues: 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.904 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 122 average time/residue: 0.1656 time to fit residues: 29.0973 Evaluate side-chains 108 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0768 time to fit residues: 1.9889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.0000 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 overall best weight: 0.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.323 7466 Z= 0.335 Angle : 0.646 18.074 10172 Z= 0.340 Chirality : 0.042 0.341 1220 Planarity : 0.007 0.145 1278 Dihedral : 6.761 103.439 1073 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.27), residues: 958 helix: 0.87 (0.22), residues: 564 sheet: -0.13 (0.76), residues: 43 loop : -2.66 (0.31), residues: 351 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.1612 time to fit residues: 26.5586 Evaluate side-chains 102 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0775 time to fit residues: 1.7720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.113 7466 Z= 0.218 Angle : 0.657 13.126 10172 Z= 0.328 Chirality : 0.042 0.355 1220 Planarity : 0.007 0.122 1278 Dihedral : 6.738 103.203 1073 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.27), residues: 958 helix: 0.95 (0.22), residues: 563 sheet: -0.12 (0.76), residues: 43 loop : -2.65 (0.32), residues: 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.783 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 110 average time/residue: 0.1631 time to fit residues: 26.2874 Evaluate side-chains 100 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0754 time to fit residues: 1.7086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.805 7466 Z= 0.938 Angle : 1.388 106.100 10172 Z= 0.583 Chirality : 0.045 0.429 1220 Planarity : 0.007 0.099 1278 Dihedral : 6.794 103.201 1073 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.46 % Favored : 91.44 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 958 helix: 0.96 (0.22), residues: 563 sheet: -0.11 (0.76), residues: 43 loop : -2.65 (0.32), residues: 352 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.996 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 98 average time/residue: 0.1570 time to fit residues: 22.6656 Evaluate side-chains 99 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0922 time to fit residues: 1.6206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 50.0000 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 0.0370 chunk 14 optimal weight: 10.0000 chunk 67 optimal weight: 0.0000 chunk 4 optimal weight: 1.9990 overall best weight: 0.5666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.199454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.176329 restraints weight = 10686.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.178996 restraints weight = 6969.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.181002 restraints weight = 4788.077| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.805 7466 Z= 0.938 Angle : 1.389 106.100 10172 Z= 0.583 Chirality : 0.045 0.429 1220 Planarity : 0.007 0.099 1278 Dihedral : 6.794 103.201 1073 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.46 % Favored : 91.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 958 helix: 0.96 (0.22), residues: 563 sheet: -0.11 (0.76), residues: 43 loop : -2.65 (0.32), residues: 352 =============================================================================== Job complete usr+sys time: 1479.58 seconds wall clock time: 27 minutes 40.46 seconds (1660.46 seconds total)