Starting phenix.real_space_refine (version: dev) on Sun Oct 3 11:03:27 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/10_2021/7v6z_31754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/10_2021/7v6z_31754.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/10_2021/7v6z_31754_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/10_2021/7v6z_31754_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/10_2021/7v6z_31754_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/10_2021/7v6z_31754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/10_2021/7v6z_31754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/10_2021/7v6z_31754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/10_2021/7v6z_31754_updated.pdb" } resolution = 3.64 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= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 772": "NH1" <-> "NH2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A ARG 1136": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4376/modules/chem_data/mon_lib" Total number of atoms: 7082 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 6984 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PTRANS': 45, 'TRANS': 962} Chain breaks: 3 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1278 Unresolved non-hydrogen dihedrals: 859 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 36, 'PHE:plan': 9, 'GLU:plan': 42, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 660 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 chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'NAG': 3, 'CLR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.45, per 1000 atoms: 0.63 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 7082 At special positions: 0 Unit cell: (88.56, 88.56, 132.84, 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 32 16.00 O 1229 8.00 N 1195 7.00 C 4626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.05 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " distance=2.02 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A1201 " - " ASN A 127 " " NAG A1202 " - " ASN A 335 " " NAG A1203 " - " ASN A 400 " " NAG B 1 " - " ASN A 986 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 2 sheets defined 59.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 61 through 103 removed outlier: 5.665A pdb=" N GLY A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 88 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 276 through 279 No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 375 through 396 removed outlier: 3.586A pdb=" N ALA A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 425 through 443 Processing helix chain 'A' and resid 453 through 477 Processing helix chain 'A' and resid 483 through 513 removed outlier: 3.865A pdb=" N LEU A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.683A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 550 removed outlier: 4.354A pdb=" N ALA A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 590 removed outlier: 3.891A pdb=" N PHE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 718 through 731 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 733 through 755 removed outlier: 3.753A pdb=" N ILE A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 766 No H-bonds generated for 'chain 'A' and resid 763 through 766' Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 803 through 814 Processing helix chain 'A' and resid 830 through 851 Processing helix chain 'A' and resid 864 through 873 Processing helix chain 'A' and resid 875 through 879 Processing helix chain 'A' and resid 905 through 914 Processing helix chain 'A' and resid 917 through 923 Processing helix chain 'A' and resid 970 through 989 Processing helix chain 'A' and resid 999 through 1033 removed outlier: 3.571A pdb=" N PHE A1003 " --> pdb=" O TYR A 999 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A1005 " --> pdb=" O PHE A1001 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLN A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TYR A1007 " --> pdb=" O PHE A1003 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A1008 " --> pdb=" O TRP A1004 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG A1011 " --> pdb=" O TYR A1007 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1060 Processing helix chain 'A' and resid 1066 through 1091 removed outlier: 3.608A pdb=" N PHE A1082 " --> pdb=" O ILE A1078 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1128 removed outlier: 3.520A pdb=" N MET A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Proline residue: A1111 - end of helix removed outlier: 3.555A pdb=" N GLY A1122 " --> pdb=" O SER A1118 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1163 removed outlier: 3.742A pdb=" N VAL A1141 " --> pdb=" O TYR A1137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A1142 " --> pdb=" O PHE A1138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A1144 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A1155 " --> pdb=" O LEU A1151 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.543A pdb=" N PHE A1163 " --> pdb=" O VAL A1159 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 345 through 351 Processing sheet with id= B, first strand: chain 'A' and resid 957 through 965 418 hydrogen bonds defined for protein. 1242 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: 2.04 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1118 1.31 - 1.44: 2015 1.44 - 1.57: 4064 1.57 - 1.70: 1 1.70 - 1.83: 50 Bond restraints: 7248 Sorted by residual: bond pdb=" C7 CLR A1204 " pdb=" C8 CLR A1204 " ideal model delta sigma weight residual 1.915 1.515 0.400 2.00e-02 2.50e+03 4.00e+02 bond pdb=" C8 CLR A1204 " pdb=" C9 CLR A1204 " ideal model delta sigma weight residual 1.174 1.523 -0.349 2.00e-02 2.50e+03 3.04e+02 bond pdb=" C10 CLR A1204 " pdb=" C9 CLR A1204 " ideal model delta sigma weight residual 1.819 1.522 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C11 CLR A1204 " pdb=" C9 CLR A1204 " ideal model delta sigma weight residual 1.782 1.532 0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C14 CLR A1204 " pdb=" C15 CLR A1204 " ideal model delta sigma weight residual 1.303 1.518 -0.215 2.00e-02 2.50e+03 1.16e+02 ... (remaining 7243 not shown) Histogram of bond angle deviations from ideal: 97.57 - 105.31: 229 105.31 - 113.04: 3865 113.04 - 120.77: 3837 120.77 - 128.50: 1965 128.50 - 136.23: 76 Bond angle restraints: 9972 Sorted by residual: angle pdb=" N LYS A 297 " pdb=" CA LYS A 297 " pdb=" C LYS A 297 " ideal model delta sigma weight residual 111.28 99.40 11.88 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N LEU A 594 " pdb=" CA LEU A 594 " pdb=" C LEU A 594 " ideal model delta sigma weight residual 111.28 122.43 -11.15 1.09e+00 8.42e-01 1.05e+02 angle pdb=" N TYR A 210 " pdb=" CA TYR A 210 " pdb=" C TYR A 210 " ideal model delta sigma weight residual 109.72 98.10 11.62 1.25e+00 6.40e-01 8.65e+01 angle pdb=" N SER A 40 " pdb=" CA SER A 40 " pdb=" C SER A 40 " ideal model delta sigma weight residual 111.74 99.44 12.30 1.35e+00 5.49e-01 8.30e+01 angle pdb=" N PHE A 729 " pdb=" CA PHE A 729 " pdb=" C PHE A 729 " ideal model delta sigma weight residual 111.07 102.04 9.03 1.07e+00 8.73e-01 7.12e+01 ... (remaining 9967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3823 17.94 - 35.89: 257 35.89 - 53.83: 81 53.83 - 71.77: 17 71.77 - 89.71: 3 Dihedral angle restraints: 4181 sinusoidal: 1254 harmonic: 2927 Sorted by residual: dihedral pdb=" CB CYS A 282 " pdb=" SG CYS A 282 " pdb=" SG CYS A 290 " pdb=" CB CYS A 290 " ideal model delta sinusoidal sigma weight residual 93.00 -177.29 -89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -36.82 -49.18 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" C ILE A 777 " pdb=" N ILE A 777 " pdb=" CA ILE A 777 " pdb=" CB ILE A 777 " ideal model delta harmonic sigma weight residual -122.00 -136.26 14.26 0 2.50e+00 1.60e-01 3.25e+01 ... (remaining 4178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.084: 1245 1.084 - 2.168: 0 2.168 - 3.251: 0 3.251 - 4.335: 0 4.335 - 5.419: 2 Chirality restraints: 1247 Sorted by residual: chirality pdb=" C8 CLR A1204 " pdb=" C14 CLR A1204 " pdb=" C7 CLR A1204 " pdb=" C9 CLR A1204 " both_signs ideal model delta sigma weight residual False -2.76 2.66 -5.42 2.00e-01 2.50e+01 7.34e+02 chirality pdb=" C13 CLR A1204 " pdb=" C12 CLR A1204 " pdb=" C14 CLR A1204 " pdb=" C17 CLR A1204 " both_signs ideal model delta sigma weight residual False 2.29 -2.69 4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" CA TRP A1004 " pdb=" N TRP A1004 " pdb=" C TRP A1004 " pdb=" CB TRP A1004 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.94e+00 ... (remaining 1244 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1157 " -0.098 5.00e-02 4.00e+02 1.47e-01 3.47e+01 pdb=" N PRO A1158 " 0.255 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1153 " 0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C GLY A1153 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY A1153 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU A1154 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 294 " 0.069 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO A 295 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.060 5.00e-02 4.00e+02 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2316 2.81 - 3.33: 7624 3.33 - 3.85: 11869 3.85 - 4.38: 13719 4.38 - 4.90: 21288 Nonbonded interactions: 56816 Sorted by model distance: nonbonded pdb=" O GLY A1115 " pdb=" OG SER A1118 " model vdw 2.282 2.440 nonbonded pdb=" CG2 ILE A1071 " pdb=" CD1 ILE A1071 " model vdw 2.314 3.104 nonbonded pdb=" N SER A1065 " pdb=" O SER A1065 " model vdw 2.354 2.496 nonbonded pdb=" N ASP A 591 " pdb=" O ASP A 591 " model vdw 2.410 2.496 nonbonded pdb=" N ARG A 772 " pdb=" N GLU A 773 " model vdw 2.436 2.560 ... (remaining 56811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. 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 32 5.16 5 C 4626 2.51 5 N 1195 2.21 5 O 1229 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 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: 0.860 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: 4.320 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 22.310 Set up NCS constraints: 0.020 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:2.050 Set ADP refinement strategy: 0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.015 0.400 7248 Z= 1.022 Angle : 1.671 12.510 9972 Z= 1.165 Chirality : 0.238 5.419 1247 Planarity : 0.011 0.147 1252 Dihedral : 14.438 88.724 2280 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.20 % Favored : 96.50 % Rotamer Outliers : 10.76 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.27), residues: 1000 helix: 2.51 (0.22), residues: 581 sheet: 0.56 (0.75), residues: 47 loop : -1.15 (0.29), residues: 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 204 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 22 residues processed: 243 average time/residue: 0.1579 time to fit residues: 53.4791 Evaluate side-chains 157 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.819 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.0706 time to fit residues: 3.8120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.0020 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 0.0170 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.5426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 154 ASN A 175 HIS A 269 ASN A 275 HIS A 296 ASN A 386 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN A 794 GLN A1006 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 7248 Z= 0.216 Angle : 0.790 24.372 9972 Z= 0.375 Chirality : 0.080 2.309 1247 Planarity : 0.007 0.098 1252 Dihedral : 5.347 42.793 1097 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Rotamer Outliers : 5.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 1000 helix: 2.15 (0.21), residues: 585 sheet: -0.03 (0.76), residues: 48 loop : -0.94 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 0.802 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 185 average time/residue: 0.1306 time to fit residues: 35.9837 Evaluate side-chains 140 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0688 time to fit residues: 2.7569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 89 optimal weight: 0.8980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7248 Z= 0.207 Angle : 0.758 25.603 9972 Z= 0.353 Chirality : 0.078 2.262 1247 Planarity : 0.006 0.073 1252 Dihedral : 5.065 49.989 1097 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Rotamer Outliers : 5.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1000 helix: 2.08 (0.21), residues: 586 sheet: -0.24 (0.80), residues: 44 loop : -0.91 (0.32), residues: 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 0.730 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 166 average time/residue: 0.1317 time to fit residues: 32.9971 Evaluate side-chains 149 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0732 time to fit residues: 3.7381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 344 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7248 Z= 0.189 Angle : 0.733 26.021 9972 Z= 0.335 Chirality : 0.077 2.242 1247 Planarity : 0.006 0.078 1252 Dihedral : 5.009 59.827 1097 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.10 % Rotamer Outliers : 2.69 % 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: 1.48 (0.28), residues: 1000 helix: 2.15 (0.22), residues: 589 sheet: -0.50 (0.75), residues: 44 loop : -0.79 (0.33), residues: 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 0.896 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 158 average time/residue: 0.1417 time to fit residues: 33.1890 Evaluate side-chains 142 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0769 time to fit residues: 2.2813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 7248 Z= 0.221 Angle : 0.745 26.170 9972 Z= 0.345 Chirality : 0.076 2.236 1247 Planarity : 0.006 0.082 1252 Dihedral : 4.975 56.823 1097 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer Outliers : 3.19 % 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: 1.32 (0.27), residues: 1000 helix: 1.98 (0.22), residues: 588 sheet: -0.63 (0.75), residues: 44 loop : -0.75 (0.33), residues: 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.901 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 147 average time/residue: 0.1350 time to fit residues: 29.8330 Evaluate side-chains 144 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0799 time to fit residues: 2.6321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 7248 Z= 0.457 Angle : 0.863 26.959 9972 Z= 0.418 Chirality : 0.079 2.211 1247 Planarity : 0.006 0.085 1252 Dihedral : 5.442 49.487 1097 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer Outliers : 5.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1000 helix: 1.27 (0.21), residues: 592 sheet: -1.39 (0.67), residues: 49 loop : -0.99 (0.33), residues: 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 157 average time/residue: 0.1344 time to fit residues: 31.8379 Evaluate side-chains 147 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0718 time to fit residues: 3.7100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 20.0000 chunk 70 optimal weight: 40.0000 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 0.0370 chunk 60 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 7248 Z= 0.244 Angle : 0.796 26.352 9972 Z= 0.362 Chirality : 0.077 2.228 1247 Planarity : 0.005 0.076 1252 Dihedral : 5.069 44.533 1097 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer Outliers : 2.69 % 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: 1000 helix: 1.57 (0.21), residues: 591 sheet: -1.18 (0.72), residues: 44 loop : -0.87 (0.34), residues: 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 0.799 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 153 average time/residue: 0.1307 time to fit residues: 30.2150 Evaluate side-chains 144 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0728 time to fit residues: 1.8204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 87 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7248 Z= 0.222 Angle : 0.786 26.305 9972 Z= 0.354 Chirality : 0.077 2.229 1247 Planarity : 0.006 0.091 1252 Dihedral : 4.859 42.578 1097 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer Outliers : 2.69 % 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: 1.04 (0.27), residues: 1000 helix: 1.76 (0.22), residues: 588 sheet: -0.92 (0.71), residues: 44 loop : -0.87 (0.33), residues: 368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 0.849 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 151 average time/residue: 0.1382 time to fit residues: 31.1750 Evaluate side-chains 146 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0842 time to fit residues: 2.3539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 40.0000 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 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 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7248 Z= 0.213 Angle : 0.788 26.312 9972 Z= 0.354 Chirality : 0.077 2.229 1247 Planarity : 0.006 0.083 1252 Dihedral : 4.772 41.171 1097 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer Outliers : 1.68 % 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: 0.92 (0.27), residues: 1000 helix: 1.65 (0.21), residues: 594 sheet: -0.86 (0.71), residues: 44 loop : -0.94 (0.33), residues: 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 0.836 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 147 average time/residue: 0.1339 time to fit residues: 29.5281 Evaluate side-chains 143 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0728 time to fit residues: 1.9151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.0670 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7248 Z= 0.192 Angle : 0.778 26.219 9972 Z= 0.350 Chirality : 0.077 2.232 1247 Planarity : 0.005 0.081 1252 Dihedral : 4.639 40.713 1097 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.10 % Rotamer Outliers : 0.17 % 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: 1000 helix: 1.72 (0.21), residues: 594 sheet: -0.56 (0.75), residues: 44 loop : -0.85 (0.33), residues: 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.807 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.1363 time to fit residues: 27.6366 Evaluate side-chains 126 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0712 time to fit residues: 1.1942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.153582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117909 restraints weight = 12671.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.121647 restraints weight = 6869.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.124281 restraints weight = 4721.800| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES. BOND : 0.006 0.051 7248 Z= 0.373 ANGLE : 0.865 26.589 9972 Z= 0.406 CHIRALITY : 0.078 2.206 1247 PLANARITY : 0.006 0.079 1252 DIHEDRAL : 5.051 38.082 1097 MIN NONBONDED DISTANCE : 2.162 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 15.27 RAMACHANDRAN PLOT: OUTLIERS : 0.10 % ALLOWED : 4.00 % FAVORED : 95.90 % ROTAMER OUTLIERS : 1.51 % 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: 0.48 (0.27), RESIDUES: 1000 HELIX: 1.19 (0.21), RESIDUES: 601 SHEET: -1.20 (0.72), RESIDUES: 44 LOOP : -0.93 (0.33), RESIDUES: 355 ------------------------------------------------------------------------------- Occupancy refinement ******************** GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES. BOND : 0.006 0.051 7248 Z= 0.373 ANGLE : 0.865 26.589 9972 Z= 0.406 CHIRALITY : 0.078 2.206 1247 PLANARITY : 0.006 0.079 1252 DIHEDRAL : 5.051 38.082 1097 MIN NONBONDED DISTANCE : 2.162 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 15.27 RAMACHANDRAN PLOT: OUTLIERS : 0.10 % ALLOWED : 4.00 % FAVORED : 95.90 % ROTAMER OUTLIERS : 1.51 % 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: 0.48 (0.27), RESIDUES: 1000 HELIX: 1.19 (0.21), RESIDUES: 601 SHEET: -1.20 (0.72), RESIDUES: 44 LOOP : -0.93 (0.33), RESIDUES: 355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 7248 Z= 0.373 Angle : 0.865 26.589 9972 Z= 0.406 Chirality : 0.078 2.206 1247 Planarity : 0.006 0.079 1252 Dihedral : 5.051 38.082 1097 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer Outliers : 1.51 % 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: 0.48 (0.27), residues: 1000 helix: 1.19 (0.21), residues: 601 sheet: -1.20 (0.72), residues: 44 loop : -0.93 (0.33), residues: 355 =============================================================================== Job complete usr+sys time: 1542.12 seconds wall clock time: 28 minutes 58.98 seconds (1738.98 seconds total)