Starting phenix.real_space_refine on Tue Feb 13 18:36:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/02_2024/6oeu_7795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/02_2024/6oeu_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_7795/02_2024/6oeu_7795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/02_2024/6oeu_7795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/02_2024/6oeu_7795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeu_7795/02_2024/6oeu_7795.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. 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-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7310 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7198 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 39, 'TRANS': 924} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 464 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 33 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 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.61, per 1000 atoms: 0.63 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 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG E 1 " - " ASN A1000 " Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.5 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: 0.81 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: 2.01 Time building geometry restraints manager: 3.37 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=" 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 angle pdb=" N PRO A 252 " pdb=" CA PRO A 252 " pdb=" CB PRO A 252 " ideal model delta sigma weight residual 103.08 110.31 -7.23 9.70e-01 1.06e+00 5.56e+01 ... (remaining 10167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 4135 21.47 - 42.93: 302 42.93 - 64.40: 41 64.40 - 85.86: 11 85.86 - 107.33: 4 Dihedral angle restraints: 4493 sinusoidal: 1693 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 4490 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 D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " 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 E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " 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 C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " 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 E 1 " -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 B 1 " model vdw 2.157 3.550 nonbonded pdb=" ND2 ASN A 414 " pdb=" O5 NAG D 1 " model vdw 2.322 2.520 nonbonded pdb=" ND2 ASN A 414 " pdb=" C2 NAG D 1 " 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.940 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.450 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 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= 0.941 Angle : 1.882 19.090 10172 Z= 1.393 Chirality : 0.112 1.665 1220 Planarity : 0.005 0.037 1278 Dihedral : 15.735 107.325 2685 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 % Allowed : 12.36 % Favored : 86.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 337 HIS 0.009 0.002 HIS A 950 PHE 0.035 0.003 PHE A 757 TYR 0.029 0.003 TYR A1001 ARG 0.010 0.001 ARG A 995 *********************** 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 : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.7103 (t0) cc_final: 0.6897 (t0) REVERT: A 520 HIS cc_start: 0.7256 (t70) cc_final: 0.6119 (m-70) REVERT: A 755 PHE cc_start: 0.6989 (t80) cc_final: 0.6789 (t80) REVERT: A 979 ASN cc_start: 0.7621 (t0) cc_final: 0.6993 (t0) REVERT: A 1004 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7130 (tp) REVERT: A 1066 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6792 (mt-10) REVERT: A 1105 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6432 (pt) outliers start: 6 outliers final: 1 residues processed: 180 average time/residue: 0.2219 time to fit residues: 52.7057 Evaluate side-chains 121 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1105 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 527 GLN A1166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7466 Z= 0.187 Angle : 0.698 10.684 10172 Z= 0.350 Chirality : 0.043 0.310 1220 Planarity : 0.004 0.047 1278 Dihedral : 9.496 80.111 1198 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.41 % Allowed : 18.61 % Favored : 78.98 % 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: -2.01 (0.26), residues: 958 helix: -0.20 (0.21), residues: 561 sheet: -1.56 (0.77), residues: 43 loop : -3.19 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 863 HIS 0.003 0.001 HIS A1099 PHE 0.030 0.002 PHE A 798 TYR 0.010 0.001 TYR A 452 ARG 0.005 0.001 ARG A 603 *********************** 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 145 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3048 (tptt) cc_final: 0.2455 (mmtm) REVERT: A 154 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8413 (p0) REVERT: A 158 MET cc_start: 0.8153 (ttp) cc_final: 0.7522 (ttm) REVERT: A 358 HIS cc_start: 0.5981 (m90) cc_final: 0.5673 (m90) REVERT: A 373 TYR cc_start: 0.7728 (t80) cc_final: 0.6812 (t80) REVERT: A 598 MET cc_start: 0.7616 (mmp) cc_final: 0.7358 (mmp) REVERT: A 602 ARG cc_start: 0.4584 (mmt180) cc_final: 0.2746 (ptp-170) REVERT: A 970 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 979 ASN cc_start: 0.7716 (t0) cc_final: 0.7355 (t0) REVERT: A 1066 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6467 (mt-10) outliers start: 17 outliers final: 8 residues processed: 139 average time/residue: 0.1606 time to fit residues: 32.1973 Evaluate side-chains 121 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 1117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.0000 chunk 87 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 154 ASN ** 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: 0.6319 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7466 Z= 0.163 Angle : 0.614 8.979 10172 Z= 0.308 Chirality : 0.042 0.348 1220 Planarity : 0.005 0.050 1278 Dihedral : 7.766 58.245 1193 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.41 % Allowed : 21.02 % Favored : 75.57 % 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: -1.28 (0.27), residues: 958 helix: 0.38 (0.22), residues: 562 sheet: -1.38 (0.77), residues: 43 loop : -2.88 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 863 HIS 0.013 0.001 HIS A 520 PHE 0.030 0.002 PHE A 798 TYR 0.017 0.001 TYR A 452 ARG 0.005 0.000 ARG A 80 *********************** 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 146 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3082 (tptt) cc_final: 0.2606 (mmtm) REVERT: A 158 MET cc_start: 0.8143 (ttp) cc_final: 0.7528 (ttm) REVERT: A 168 ASN cc_start: 0.4316 (t0) cc_final: 0.3783 (m-40) REVERT: A 372 MET cc_start: 0.8289 (tpp) cc_final: 0.7909 (ttm) REVERT: A 373 TYR cc_start: 0.7692 (t80) cc_final: 0.6696 (t80) REVERT: A 598 MET cc_start: 0.7620 (mmp) cc_final: 0.7378 (mmp) REVERT: A 602 ARG cc_start: 0.4393 (mmt180) cc_final: 0.2622 (ptp-170) REVERT: A 796 LYS cc_start: 0.8260 (ttmt) cc_final: 0.8046 (ttpt) REVERT: A 979 ASN cc_start: 0.7836 (t0) cc_final: 0.7596 (t0) outliers start: 24 outliers final: 13 residues processed: 138 average time/residue: 0.1573 time to fit residues: 31.0751 Evaluate side-chains 126 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 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 177 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7466 Z= 0.157 Angle : 0.587 8.064 10172 Z= 0.291 Chirality : 0.041 0.327 1220 Planarity : 0.004 0.048 1278 Dihedral : 7.120 59.106 1193 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.12 % Allowed : 21.88 % Favored : 74.01 % 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: -0.94 (0.27), residues: 958 helix: 0.66 (0.22), residues: 568 sheet: -0.98 (0.79), residues: 43 loop : -2.82 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 863 HIS 0.004 0.001 HIS A 950 PHE 0.028 0.001 PHE A 798 TYR 0.010 0.001 TYR A 452 ARG 0.004 0.000 ARG A 80 *********************** 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 149 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3033 (tptt) cc_final: 0.2778 (mmtm) REVERT: A 120 ASN cc_start: 0.6813 (m-40) cc_final: 0.6599 (m110) REVERT: A 158 MET cc_start: 0.8007 (ttp) cc_final: 0.7384 (ttm) REVERT: A 168 ASN cc_start: 0.4651 (t0) cc_final: 0.4086 (m-40) REVERT: A 200 GLU cc_start: 0.8510 (tp30) cc_final: 0.8251 (tp30) REVERT: A 373 TYR cc_start: 0.7621 (t80) cc_final: 0.6632 (t80) REVERT: A 598 MET cc_start: 0.7590 (mmp) cc_final: 0.7116 (mmt) REVERT: A 602 ARG cc_start: 0.4182 (mmt180) cc_final: 0.2324 (ptp-170) REVERT: A 979 ASN cc_start: 0.7865 (t0) cc_final: 0.7664 (t0) outliers start: 29 outliers final: 18 residues processed: 140 average time/residue: 0.1610 time to fit residues: 32.4650 Evaluate side-chains 130 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 0.0040 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7466 Z= 0.207 Angle : 0.615 8.961 10172 Z= 0.303 Chirality : 0.042 0.346 1220 Planarity : 0.004 0.047 1278 Dihedral : 7.093 54.322 1193 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.97 % Allowed : 22.30 % Favored : 72.73 % 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: -0.87 (0.27), residues: 958 helix: 0.68 (0.22), residues: 562 sheet: -0.78 (0.80), residues: 45 loop : -2.72 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 863 HIS 0.004 0.001 HIS A 950 PHE 0.030 0.002 PHE A 798 TYR 0.021 0.001 TYR A 452 ARG 0.008 0.000 ARG A 80 *********************** 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 152 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3044 (tptt) cc_final: 0.2789 (mmtm) REVERT: A 120 ASN cc_start: 0.6797 (m-40) cc_final: 0.6533 (m110) REVERT: A 158 MET cc_start: 0.8079 (ttp) cc_final: 0.7467 (ttm) REVERT: A 168 ASN cc_start: 0.3908 (t0) cc_final: 0.3459 (m-40) REVERT: A 372 MET cc_start: 0.8244 (tpp) cc_final: 0.7887 (ttm) REVERT: A 373 TYR cc_start: 0.7560 (t80) cc_final: 0.6432 (t80) REVERT: A 598 MET cc_start: 0.7582 (mmp) cc_final: 0.7184 (mmt) REVERT: A 602 ARG cc_start: 0.4229 (mmt180) cc_final: 0.2398 (ptp-170) outliers start: 35 outliers final: 30 residues processed: 140 average time/residue: 0.1525 time to fit residues: 31.1800 Evaluate side-chains 137 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1145 PHE Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 54 optimal weight: 0.0980 chunk 22 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 89 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7466 Z= 0.148 Angle : 0.587 8.204 10172 Z= 0.285 Chirality : 0.040 0.316 1220 Planarity : 0.004 0.046 1278 Dihedral : 6.596 53.889 1193 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.12 % Allowed : 25.14 % Favored : 70.74 % 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 (0.28), residues: 958 helix: 0.85 (0.22), residues: 573 sheet: -0.57 (0.80), residues: 45 loop : -2.65 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 863 HIS 0.003 0.001 HIS A 950 PHE 0.018 0.001 PHE A 798 TYR 0.020 0.001 TYR A 452 ARG 0.005 0.000 ARG A 144 *********************** 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 150 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.2974 (tptt) cc_final: 0.2753 (mmtm) REVERT: A 120 ASN cc_start: 0.6777 (m-40) cc_final: 0.6533 (m110) REVERT: A 144 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7409 (ttm110) REVERT: A 158 MET cc_start: 0.7995 (ttp) cc_final: 0.7373 (ttm) REVERT: A 168 ASN cc_start: 0.4350 (t0) cc_final: 0.4036 (m-40) REVERT: A 373 TYR cc_start: 0.7539 (t80) cc_final: 0.6542 (t80) REVERT: A 575 LEU cc_start: 0.7188 (mm) cc_final: 0.6887 (mm) REVERT: A 598 MET cc_start: 0.7457 (mmp) cc_final: 0.7035 (mmt) REVERT: A 602 ARG cc_start: 0.4155 (mmt180) cc_final: 0.2253 (ptp-170) REVERT: A 1086 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6337 (mp) outliers start: 29 outliers final: 22 residues processed: 144 average time/residue: 0.1687 time to fit residues: 34.3377 Evaluate side-chains 138 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7466 Z= 0.181 Angle : 0.612 12.031 10172 Z= 0.294 Chirality : 0.041 0.325 1220 Planarity : 0.004 0.046 1278 Dihedral : 6.429 53.597 1193 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.55 % Allowed : 25.71 % Favored : 69.74 % 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: -0.60 (0.28), residues: 958 helix: 0.86 (0.22), residues: 574 sheet: -0.47 (0.80), residues: 45 loop : -2.67 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 948 HIS 0.004 0.001 HIS A 950 PHE 0.021 0.001 PHE A 798 TYR 0.022 0.001 TYR A 452 ARG 0.005 0.000 ARG A 80 *********************** 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 147 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3044 (tptt) cc_final: 0.2827 (mmtm) REVERT: A 120 ASN cc_start: 0.6714 (m-40) cc_final: 0.6461 (m110) REVERT: A 158 MET cc_start: 0.8042 (ttp) cc_final: 0.7420 (ttm) REVERT: A 373 TYR cc_start: 0.7541 (t80) cc_final: 0.6591 (t80) REVERT: A 575 LEU cc_start: 0.7324 (mm) cc_final: 0.7085 (mm) REVERT: A 598 MET cc_start: 0.7422 (mmp) cc_final: 0.7028 (mmt) REVERT: A 602 ARG cc_start: 0.4089 (mmt180) cc_final: 0.2203 (ptp-170) REVERT: A 802 ASN cc_start: 0.7632 (p0) cc_final: 0.7209 (t0) outliers start: 32 outliers final: 28 residues processed: 139 average time/residue: 0.1617 time to fit residues: 31.7699 Evaluate side-chains 138 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7466 Z= 0.192 Angle : 0.612 12.373 10172 Z= 0.296 Chirality : 0.042 0.338 1220 Planarity : 0.004 0.047 1278 Dihedral : 6.308 53.264 1193 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.26 % Allowed : 25.14 % Favored : 69.60 % 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: -0.59 (0.28), residues: 958 helix: 0.89 (0.22), residues: 574 sheet: -0.45 (0.80), residues: 43 loop : -2.71 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1027 HIS 0.004 0.001 HIS A 950 PHE 0.020 0.001 PHE A 798 TYR 0.023 0.001 TYR A 452 ARG 0.004 0.000 ARG A 80 *********************** 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 146 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3033 (tptt) cc_final: 0.2829 (mmtm) REVERT: A 120 ASN cc_start: 0.6638 (m-40) cc_final: 0.6391 (m110) REVERT: A 158 MET cc_start: 0.8046 (ttp) cc_final: 0.7419 (ttm) REVERT: A 373 TYR cc_start: 0.7410 (t80) cc_final: 0.6431 (t80) REVERT: A 598 MET cc_start: 0.7435 (mmp) cc_final: 0.7076 (mmt) REVERT: A 602 ARG cc_start: 0.3892 (mmt180) cc_final: 0.1979 (ptp-170) REVERT: A 802 ASN cc_start: 0.7684 (p0) cc_final: 0.7314 (t0) REVERT: A 947 GLU cc_start: 0.5808 (mt-10) cc_final: 0.5150 (tt0) REVERT: A 970 GLU cc_start: 0.7788 (tt0) cc_final: 0.7474 (tt0) REVERT: A 1086 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6248 (mp) outliers start: 37 outliers final: 28 residues processed: 136 average time/residue: 0.1523 time to fit residues: 30.0413 Evaluate side-chains 135 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1122 MET Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0670 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7466 Z= 0.170 Angle : 0.620 13.561 10172 Z= 0.299 Chirality : 0.042 0.360 1220 Planarity : 0.004 0.046 1278 Dihedral : 6.171 53.463 1193 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.40 % Allowed : 26.85 % Favored : 68.75 % 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: -0.42 (0.28), residues: 958 helix: 1.03 (0.22), residues: 573 sheet: -0.53 (0.80), residues: 43 loop : -2.61 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 948 HIS 0.007 0.001 HIS A 950 PHE 0.018 0.001 PHE A 798 TYR 0.023 0.001 TYR A 452 ARG 0.008 0.000 ARG A 80 *********************** 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 139 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3053 (tptt) cc_final: 0.2841 (mmtm) REVERT: A 120 ASN cc_start: 0.6619 (m-40) cc_final: 0.6376 (m110) REVERT: A 158 MET cc_start: 0.8016 (ttp) cc_final: 0.7387 (ttm) REVERT: A 373 TYR cc_start: 0.7471 (t80) cc_final: 0.6636 (t80) REVERT: A 598 MET cc_start: 0.7368 (mmp) cc_final: 0.7103 (mmt) REVERT: A 802 ASN cc_start: 0.7487 (p0) cc_final: 0.7173 (t0) REVERT: A 920 TYR cc_start: 0.8378 (m-10) cc_final: 0.8169 (m-10) REVERT: A 947 GLU cc_start: 0.5762 (mt-10) cc_final: 0.5302 (tt0) REVERT: A 970 GLU cc_start: 0.7817 (tt0) cc_final: 0.7454 (tt0) REVERT: A 1004 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6833 (tp) outliers start: 31 outliers final: 26 residues processed: 129 average time/residue: 0.1505 time to fit residues: 28.3350 Evaluate side-chains 135 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1122 MET Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7466 Z= 0.184 Angle : 0.629 14.161 10172 Z= 0.304 Chirality : 0.042 0.377 1220 Planarity : 0.004 0.047 1278 Dihedral : 6.088 53.239 1193 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.26 % Allowed : 26.99 % Favored : 68.75 % 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: -0.32 (0.28), residues: 958 helix: 1.12 (0.22), residues: 568 sheet: -0.54 (0.81), residues: 43 loop : -2.54 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 948 HIS 0.004 0.001 HIS A 950 PHE 0.039 0.001 PHE A 798 TYR 0.023 0.001 TYR A 452 ARG 0.007 0.000 ARG A 80 ********************** 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 138 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3051 (tptt) cc_final: 0.2846 (mmtm) REVERT: A 120 ASN cc_start: 0.6593 (m-40) cc_final: 0.6184 (m110) REVERT: A 158 MET cc_start: 0.8037 (ttp) cc_final: 0.7425 (ttm) REVERT: A 373 TYR cc_start: 0.7385 (t80) cc_final: 0.6537 (t80) REVERT: A 414 ASN cc_start: 0.5462 (m-40) cc_final: 0.4135 (t0) REVERT: A 598 MET cc_start: 0.7396 (mmp) cc_final: 0.7139 (mmt) REVERT: A 802 ASN cc_start: 0.7542 (p0) cc_final: 0.7278 (t0) REVERT: A 947 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5455 (tt0) REVERT: A 970 GLU cc_start: 0.7801 (tt0) cc_final: 0.7499 (tt0) REVERT: A 1004 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6770 (tp) REVERT: A 1086 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6395 (mt) outliers start: 30 outliers final: 27 residues processed: 129 average time/residue: 0.1542 time to fit residues: 29.2725 Evaluate side-chains 134 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1122 MET Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.0770 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 76 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 14 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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** A1099 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.202534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178438 restraints weight = 10614.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.181605 restraints weight = 6812.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.183696 restraints weight = 4668.161| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7466 Z= 0.148 Angle : 0.602 13.469 10172 Z= 0.290 Chirality : 0.041 0.365 1220 Planarity : 0.004 0.045 1278 Dihedral : 5.869 53.525 1193 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.12 % Allowed : 27.27 % Favored : 68.61 % 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: -0.11 (0.28), residues: 958 helix: 1.29 (0.22), residues: 567 sheet: -0.49 (0.82), residues: 43 loop : -2.44 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 948 HIS 0.003 0.001 HIS A 823 PHE 0.028 0.001 PHE A 798 TYR 0.024 0.001 TYR A 452 ARG 0.007 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1649.52 seconds wall clock time: 30 minutes 48.84 seconds (1848.84 seconds total)