Starting phenix.real_space_refine (version: dev) on Mon Apr 4 15:34:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/04_2022/7v6z_31754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/04_2022/7v6z_31754.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/04_2022/7v6z_31754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/04_2022/7v6z_31754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/04_2022/7v6z_31754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6z_31754/04_2022/7v6z_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 Assert all atoms have isotropic ADPs 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-4553/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: 4.88, per 1000 atoms: 0.69 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 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1201 " - " ASN A 127 " " NAG A1202 " - " ASN A 335 " " NAG A1203 " - " ASN A 400 " " NAG B 1 " - " ASN A 986 " Time building additional restraints: 3.14 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: 1.13 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: 2.23 Time building geometry restraints manager: 3.38 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=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.26e-02 6.30e+03 4.50e+01 bond pdb=" C VAL A 393 " pdb=" O VAL A 393 " ideal model delta sigma weight residual 1.237 1.313 -0.076 1.17e-02 7.31e+03 4.24e+01 bond pdb=" CA TYR A 774 " pdb=" C TYR A 774 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.29e-02 6.01e+03 4.01e+01 bond pdb=" N SER A 172 " pdb=" CA SER A 172 " ideal model delta sigma weight residual 1.459 1.386 0.073 1.21e-02 6.83e+03 3.64e+01 bond pdb=" CA ALA A 921 " pdb=" C ALA A 921 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.30e-02 5.92e+03 3.27e+01 ... (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: 3827 17.94 - 35.89: 255 35.89 - 53.83: 80 53.83 - 71.77: 17 71.77 - 89.71: 3 Dihedral angle restraints: 4182 sinusoidal: 1255 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 4179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 975 0.120 - 0.239: 206 0.239 - 0.359: 49 0.359 - 0.479: 13 0.479 - 0.598: 4 Chirality restraints: 1247 Sorted by residual: 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 chirality pdb=" CA ILE A 777 " pdb=" N ILE A 777 " pdb=" C ILE A 777 " pdb=" CB ILE A 777 " both_signs ideal model delta sigma weight residual False 2.43 1.90 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA LEU A 594 " pdb=" N LEU A 594 " pdb=" C LEU A 594 " pdb=" CB LEU A 594 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.84e+00 ... (remaining 1244 not shown) Planarity restraints: 1255 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 1252 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. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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 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: 0.690 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: 4.410 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 23.380 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.012 0.085 7248 Z= 0.790 Angle : 1.661 12.301 9972 Z= 1.163 Chirality : 0.114 0.598 1247 Planarity : 0.010 0.147 1251 Dihedral : 14.371 88.724 2281 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.74 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 : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 22 residues processed: 243 average time/residue: 0.1537 time to fit residues: 52.0727 Evaluate side-chains 157 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.808 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.0682 time to fit residues: 3.8667 ------------------------------------------------------------------------------- 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: 7.9990 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 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 296 ASN A 386 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN A 794 GLN A1006 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 7248 Z= 0.238 Angle : 0.721 10.466 9972 Z= 0.382 Chirality : 0.046 0.242 1247 Planarity : 0.007 0.094 1251 Dihedral : 5.187 26.309 1098 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.90 % Rotamer Outliers : 6.22 % 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: 1.03 (0.26), residues: 1000 helix: 1.78 (0.21), residues: 587 sheet: -0.19 (0.72), residues: 48 loop : -1.03 (0.31), residues: 365 *********************** 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 194 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 0.791 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 181 average time/residue: 0.1313 time to fit residues: 35.2775 Evaluate side-chains 152 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0870 time to fit residues: 4.3484 ------------------------------------------------------------------------------- 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: 5.9990 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 72 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** 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: 0.7132 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7248 Z= 0.217 Angle : 0.696 13.527 9972 Z= 0.353 Chirality : 0.043 0.223 1247 Planarity : 0.006 0.070 1251 Dihedral : 4.933 24.593 1098 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.70 % Rotamer Outliers : 4.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1000 helix: 1.83 (0.21), residues: 586 sheet: -0.40 (0.74), residues: 49 loop : -1.00 (0.32), residues: 365 *********************** 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 179 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 0.799 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 165 average time/residue: 0.1310 time to fit residues: 32.5301 Evaluate side-chains 142 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0704 time to fit residues: 2.9864 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 0.0060 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7248 Z= 0.203 Angle : 0.634 10.334 9972 Z= 0.320 Chirality : 0.042 0.217 1247 Planarity : 0.006 0.072 1251 Dihedral : 4.752 22.421 1098 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.70 % Rotamer Outliers : 3.87 % 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: 1.03 (0.27), residues: 1000 helix: 1.83 (0.21), residues: 583 sheet: -0.64 (0.75), residues: 44 loop : -1.01 (0.31), residues: 373 *********************** 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 167 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 0.795 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 155 average time/residue: 0.1361 time to fit residues: 31.3430 Evaluate side-chains 143 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0762 time to fit residues: 3.1896 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.0270 chunk 87 optimal weight: 0.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7171 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7248 Z= 0.199 Angle : 0.641 10.128 9972 Z= 0.320 Chirality : 0.041 0.281 1247 Planarity : 0.005 0.078 1251 Dihedral : 4.668 20.552 1098 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.70 % Rotamer Outliers : 2.35 % 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: 1.02 (0.27), residues: 1000 helix: 1.83 (0.21), residues: 584 sheet: -0.60 (0.74), residues: 42 loop : -1.05 (0.32), residues: 374 *********************** 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 163 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.054 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 154 average time/residue: 0.1429 time to fit residues: 33.1676 Evaluate side-chains 147 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0736 time to fit residues: 2.3476 ------------------------------------------------------------------------------- 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: 30.0000 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS A 487 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN A 809 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.151 7248 Z= 0.359 Angle : 0.725 7.806 9972 Z= 0.376 Chirality : 0.044 0.261 1247 Planarity : 0.007 0.080 1251 Dihedral : 4.907 23.703 1098 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer Outliers : 5.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1000 helix: 1.32 (0.21), residues: 592 sheet: -1.50 (0.66), residues: 49 loop : -0.97 (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 178 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 0.835 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 163 average time/residue: 0.1352 time to fit residues: 32.7848 Evaluate side-chains 152 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0739 time to fit residues: 3.5796 ------------------------------------------------------------------------------- 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: 10.0000 chunk 70 optimal weight: 40.0000 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 788 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 7248 Z= 0.295 Angle : 0.672 9.136 9972 Z= 0.343 Chirality : 0.042 0.290 1247 Planarity : 0.006 0.080 1251 Dihedral : 4.877 23.203 1098 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer Outliers : 2.52 % 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 (0.27), residues: 1000 helix: 1.36 (0.21), residues: 593 sheet: -0.93 (0.74), residues: 42 loop : -1.04 (0.33), 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: 15 poor density : 143 time to evaluate : 0.822 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 151 average time/residue: 0.1315 time to fit residues: 30.0245 Evaluate side-chains 147 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0708 time to fit residues: 2.7593 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 0.0370 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS A 487 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 7248 Z= 0.239 Angle : 0.659 10.159 9972 Z= 0.328 Chirality : 0.042 0.293 1247 Planarity : 0.006 0.084 1251 Dihedral : 4.732 22.600 1098 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % 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: 0.70 (0.27), residues: 1000 helix: 1.44 (0.21), residues: 594 sheet: -0.78 (0.74), residues: 42 loop : -0.99 (0.33), residues: 364 *********************** 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 151 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 0.807 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 147 average time/residue: 0.1374 time to fit residues: 30.2225 Evaluate side-chains 140 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0738 time to fit residues: 1.6766 ------------------------------------------------------------------------------- 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: 6.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 40.0000 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7299 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7248 Z= 0.223 Angle : 0.677 10.694 9972 Z= 0.333 Chirality : 0.042 0.303 1247 Planarity : 0.006 0.080 1251 Dihedral : 4.643 22.317 1098 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer Outliers : 1.34 % 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: 0.67 (0.27), residues: 1000 helix: 1.40 (0.21), residues: 600 sheet: -0.70 (0.73), residues: 42 loop : -1.04 (0.33), residues: 358 *********************** 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 151 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 0.803 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 145 average time/residue: 0.1367 time to fit residues: 30.1581 Evaluate side-chains 144 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0930 time to fit residues: 2.3232 ------------------------------------------------------------------------------- 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: 0.6980 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.0370 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.0060 chunk 24 optimal weight: 0.5980 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7248 Z= 0.186 Angle : 0.664 12.738 9972 Z= 0.323 Chirality : 0.041 0.321 1247 Planarity : 0.006 0.101 1251 Dihedral : 4.448 20.502 1098 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer Outliers : 1.18 % 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: 594 sheet: -0.52 (0.74), residues: 42 loop : -0.99 (0.32), residues: 364 ********************** 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 157 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 0.838 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 152 average time/residue: 0.1357 time to fit residues: 31.0378 Evaluate side-chains 142 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0746 time to fit residues: 1.7728 ------------------------------------------------------------------------------- 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: 20.0000 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.160082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.124519 restraints weight = 12055.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.128731 restraints weight = 6196.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.131504 restraints weight = 4107.532| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 7248 Z= 0.238 Angle : 0.679 11.568 9972 Z= 0.336 Chirality : 0.042 0.310 1247 Planarity : 0.006 0.091 1251 Dihedral : 4.438 19.578 1098 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1000 helix: 1.52 (0.21), residues: 595 sheet: -0.48 (0.76), residues: 42 loop : -1.03 (0.32), residues: 363 =============================================================================== Job complete usr+sys time: 1563.55 seconds wall clock time: 29 minutes 1.04 seconds (1741.04 seconds total)