Starting phenix.real_space_refine on Sun Dec 10 13:57:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/12_2023/7pzr_13736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/12_2023/7pzr_13736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/12_2023/7pzr_13736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/12_2023/7pzr_13736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/12_2023/7pzr_13736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/12_2023/7pzr_13736.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.007 sd= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7365 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4712 2.51 5 N 1336 2.21 5 O 1307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7404 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7404 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 935, 7362 Classifications: {'peptide': 935} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 61, 'TRANS': 873} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 935, 7362 Classifications: {'peptide': 935} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 61, 'TRANS': 873} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 7485 Time building chain proxies: 7.30, per 1000 atoms: 0.99 Number of scatterers: 7404 At special positions: 0 Unit cell: (81.81, 93.93, 103.02, 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 49 16.00 O 1307 8.00 N 1336 7.00 C 4712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 2.4 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 68.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 220 through 237 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 340 through 354 Processing helix chain 'A' and resid 371 through 376 removed outlier: 4.116A pdb=" N ASP A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 424 through 463 Processing helix chain 'A' and resid 467 through 474 removed outlier: 4.030A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 490 Processing helix chain 'A' and resid 497 through 521 Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.810A pdb=" N LEU A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 568 through 587 Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 688 through 705 removed outlier: 3.918A pdb=" N ALA A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 836 through 850 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 883 through 888 Processing helix chain 'A' and resid 890 through 907 Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 954 through 973 Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 986 through 999 Processing helix chain 'A' and resid 1003 through 1017 removed outlier: 4.424A pdb=" N ARG A1007 " --> pdb=" O ARG A1003 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1044 Processing helix chain 'A' and resid 1044 through 1065 Processing helix chain 'A' and resid 1111 through 1143 Proline residue: A1120 - end of helix Processing helix chain 'A' and resid 1156 through 1177 removed outlier: 4.318A pdb=" N SER A1161 " --> pdb=" O ALA A1157 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1172 " --> pdb=" O ARG A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1192 Processing helix chain 'A' and resid 1201 through 1210 Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.664A pdb=" N ARG A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1229 removed outlier: 4.093A pdb=" N PHE A1229 " --> pdb=" O THR A1226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1226 through 1229' Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496 Processing sheet with id=AA3, first strand: chain 'A' and resid 794 through 795 Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AA5, first strand: chain 'A' and resid 919 through 921 Processing sheet with id=AA6, first strand: chain 'A' and resid 1069 through 1071 484 hydrogen bonds defined for protein. 1434 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: 2.58 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1599 1.33 - 1.45: 1602 1.45 - 1.57: 4309 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 7585 Sorted by residual: bond pdb=" CB ILE A1124 " pdb=" CG1 ILE A1124 " ideal model delta sigma weight residual 1.530 1.498 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" CG1 ILE A1124 " pdb=" CD1 ILE A1124 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.21e+00 bond pdb=" CB ASN A 799 " pdb=" CG ASN A 799 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.18e+00 bond pdb=" CG LEU A 490 " pdb=" CD2 LEU A 490 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CB VAL A1149 " pdb=" CG2 VAL A1149 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 ... (remaining 7580 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.00: 320 107.00 - 113.75: 4242 113.75 - 120.49: 2837 120.49 - 127.24: 2794 127.24 - 133.99: 113 Bond angle restraints: 10306 Sorted by residual: angle pdb=" N PHE A1229 " pdb=" CA PHE A1229 " pdb=" CB PHE A1229 " ideal model delta sigma weight residual 110.68 119.51 -8.83 1.68e+00 3.54e-01 2.76e+01 angle pdb=" N ARG A 273 " pdb=" CA ARG A 273 " pdb=" C ARG A 273 " ideal model delta sigma weight residual 113.97 109.29 4.68 1.28e+00 6.10e-01 1.34e+01 angle pdb=" C ARG A 273 " pdb=" N GLN A 274 " pdb=" CA GLN A 274 " ideal model delta sigma weight residual 121.52 127.19 -5.67 1.84e+00 2.95e-01 9.51e+00 angle pdb=" C GLY A 923 " pdb=" N SER A 924 " pdb=" CA SER A 924 " ideal model delta sigma weight residual 121.54 127.35 -5.81 1.91e+00 2.74e-01 9.25e+00 angle pdb=" N GLY A 521 " pdb=" CA GLY A 521 " pdb=" C GLY A 521 " ideal model delta sigma weight residual 115.64 111.30 4.34 1.46e+00 4.69e-01 8.83e+00 ... (remaining 10301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4251 17.83 - 35.66: 315 35.66 - 53.48: 52 53.48 - 71.31: 12 71.31 - 89.14: 3 Dihedral angle restraints: 4633 sinusoidal: 1873 harmonic: 2760 Sorted by residual: dihedral pdb=" N PHE A1229 " pdb=" C PHE A1229 " pdb=" CA PHE A1229 " pdb=" CB PHE A1229 " ideal model delta harmonic sigma weight residual 122.80 130.61 -7.81 0 2.50e+00 1.60e-01 9.75e+00 dihedral pdb=" CB AMET A 671 " pdb=" CG AMET A 671 " pdb=" SD AMET A 671 " pdb=" CE AMET A 671 " ideal model delta sinusoidal sigma weight residual 60.00 119.68 -59.68 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 967 " pdb=" CB ARG A 967 " pdb=" CG ARG A 967 " pdb=" CD ARG A 967 " ideal model delta sinusoidal sigma weight residual -180.00 -130.70 -49.30 3 1.50e+01 4.44e-03 8.76e+00 ... (remaining 4630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 881 0.043 - 0.086: 187 0.086 - 0.129: 64 0.129 - 0.172: 11 0.172 - 0.216: 5 Chirality restraints: 1148 Sorted by residual: chirality pdb=" CB VAL A1149 " pdb=" CA VAL A1149 " pdb=" CG1 VAL A1149 " pdb=" CG2 VAL A1149 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU A 473 " pdb=" CB LEU A 473 " pdb=" CD1 LEU A 473 " pdb=" CD2 LEU A 473 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CB VAL A 867 " pdb=" CA VAL A 867 " pdb=" CG1 VAL A 867 " pdb=" CG2 VAL A 867 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 1145 not shown) Planarity restraints: 1337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1229 " 0.049 2.00e-02 2.50e+03 4.54e-02 3.61e+01 pdb=" CG PHE A1229 " -0.105 2.00e-02 2.50e+03 pdb=" CD1 PHE A1229 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A1229 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A1229 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A1229 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A1229 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 512 " -0.030 2.00e-02 2.50e+03 2.78e-02 1.16e+01 pdb=" CG HIS A 512 " 0.059 2.00e-02 2.50e+03 pdb=" ND1 HIS A 512 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS A 512 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 512 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 512 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1167 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C CYS A1167 " 0.054 2.00e-02 2.50e+03 pdb=" O CYS A1167 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A1168 " -0.018 2.00e-02 2.50e+03 ... (remaining 1334 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 25 2.63 - 3.20: 6794 3.20 - 3.76: 12635 3.76 - 4.33: 17269 4.33 - 4.90: 27323 Nonbonded interactions: 64046 Sorted by model distance: nonbonded pdb=" OE1 GLU A 900 " pdb=" OH TYR A 913 " model vdw 2.062 2.440 nonbonded pdb=" O VAL A 963 " pdb=" NE2 GLN A1035 " model vdw 2.156 2.520 nonbonded pdb=" OD1 ASN A 528 " pdb=" NH2 ARG A 531 " model vdw 2.215 2.520 nonbonded pdb=" ND2 ASN A 369 " pdb=" O THR A 690 " model vdw 2.276 2.520 nonbonded pdb=" O LEU A 235 " pdb=" NH2 ARG A 516 " model vdw 2.295 2.520 ... (remaining 64041 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 2.170 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.230 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 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 : 0.004 0.058 7585 Z= 0.242 Angle : 0.706 8.828 10306 Z= 0.417 Chirality : 0.043 0.216 1148 Planarity : 0.005 0.075 1337 Dihedral : 12.708 89.141 2841 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 3.84 (0.27), residues: 930 helix: 3.32 (0.20), residues: 626 sheet: 0.96 (1.13), residues: 23 loop : 0.89 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 892 HIS 0.025 0.003 HIS A 512 PHE 0.105 0.003 PHE A1229 TYR 0.043 0.002 TYR A 610 ARG 0.016 0.001 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 1.2662 time to fit residues: 316.1445 Evaluate side-chains 123 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7585 Z= 0.268 Angle : 0.732 10.838 10306 Z= 0.365 Chirality : 0.039 0.152 1148 Planarity : 0.006 0.070 1337 Dihedral : 4.165 39.880 1035 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.42 % Allowed : 17.36 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.26), residues: 930 helix: 2.47 (0.20), residues: 637 sheet: 0.34 (0.86), residues: 33 loop : 0.64 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A1154 HIS 0.010 0.002 HIS A 512 PHE 0.050 0.003 PHE A 802 TYR 0.015 0.002 TYR A1031 ARG 0.008 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 8 residues processed: 142 average time/residue: 0.9926 time to fit residues: 151.1535 Evaluate side-chains 98 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.6499 time to fit residues: 3.3319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS A1009 GLN A1035 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7585 Z= 0.230 Angle : 0.717 13.410 10306 Z= 0.346 Chirality : 0.038 0.134 1148 Planarity : 0.005 0.049 1337 Dihedral : 4.129 35.317 1035 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.30 % Allowed : 20.28 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.27), residues: 930 helix: 2.25 (0.20), residues: 627 sheet: -0.04 (0.86), residues: 35 loop : 0.62 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 567 HIS 0.006 0.001 HIS A 920 PHE 0.033 0.003 PHE A 277 TYR 0.027 0.002 TYR A 533 ARG 0.008 0.001 ARG A 936 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 123 average time/residue: 0.9993 time to fit residues: 132.1289 Evaluate side-chains 104 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.7663 time to fit residues: 3.7528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 304 GLN ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN A1035 GLN A1164 ASN A1170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7585 Z= 0.226 Angle : 0.735 14.606 10306 Z= 0.343 Chirality : 0.038 0.192 1148 Planarity : 0.005 0.074 1337 Dihedral : 4.058 34.704 1035 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.68 % Allowed : 20.41 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.27), residues: 930 helix: 2.22 (0.20), residues: 621 sheet: 0.04 (0.87), residues: 35 loop : 0.77 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1154 HIS 0.005 0.001 HIS A1156 PHE 0.032 0.002 PHE A 465 TYR 0.028 0.002 TYR A 533 ARG 0.010 0.001 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 120 average time/residue: 0.8631 time to fit residues: 112.4327 Evaluate side-chains 103 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.3707 time to fit residues: 3.3827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 37 optimal weight: 0.0870 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 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 0.055 7585 Z= 0.204 Angle : 0.728 14.703 10306 Z= 0.331 Chirality : 0.039 0.354 1148 Planarity : 0.005 0.064 1337 Dihedral : 4.041 36.016 1035 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.17 % Allowed : 21.55 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.27), residues: 930 helix: 2.22 (0.21), residues: 620 sheet: 0.12 (0.89), residues: 35 loop : 0.82 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 567 HIS 0.004 0.001 HIS A 624 PHE 0.033 0.002 PHE A 277 TYR 0.031 0.002 TYR A 533 ARG 0.010 0.001 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 120 average time/residue: 0.8947 time to fit residues: 116.0872 Evaluate side-chains 107 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1765 time to fit residues: 1.6795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7585 Z= 0.217 Angle : 0.758 14.159 10306 Z= 0.346 Chirality : 0.039 0.352 1148 Planarity : 0.005 0.060 1337 Dihedral : 4.068 35.258 1035 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.79 % Allowed : 23.32 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.27), residues: 930 helix: 2.13 (0.21), residues: 620 sheet: 0.03 (0.89), residues: 35 loop : 0.75 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 567 HIS 0.004 0.001 HIS A 624 PHE 0.031 0.002 PHE A 465 TYR 0.025 0.002 TYR A 468 ARG 0.007 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 113 average time/residue: 0.8944 time to fit residues: 109.3991 Evaluate side-chains 101 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1754 time to fit residues: 1.7042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 50 optimal weight: 0.0370 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7585 Z= 0.216 Angle : 0.763 13.847 10306 Z= 0.351 Chirality : 0.040 0.345 1148 Planarity : 0.005 0.053 1337 Dihedral : 4.099 36.218 1035 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.30 % Allowed : 23.70 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.27), residues: 930 helix: 2.05 (0.21), residues: 621 sheet: 0.02 (0.89), residues: 35 loop : 0.71 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1154 HIS 0.004 0.001 HIS A 624 PHE 0.036 0.002 PHE A 465 TYR 0.020 0.002 TYR A 468 ARG 0.008 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 110 average time/residue: 0.8690 time to fit residues: 103.8525 Evaluate side-chains 96 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.4890 time to fit residues: 2.8723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 17 optimal weight: 0.0170 chunk 56 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 44 optimal weight: 0.0030 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.1766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7585 Z= 0.212 Angle : 0.776 13.950 10306 Z= 0.354 Chirality : 0.040 0.287 1148 Planarity : 0.005 0.067 1337 Dihedral : 4.118 39.232 1035 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.66 % Allowed : 25.10 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.27), residues: 930 helix: 2.01 (0.21), residues: 621 sheet: 0.07 (0.89), residues: 35 loop : 0.70 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP A 441 HIS 0.005 0.001 HIS A1030 PHE 0.043 0.002 PHE A 465 TYR 0.016 0.001 TYR A 468 ARG 0.016 0.001 ARG A1007 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 116 average time/residue: 0.9505 time to fit residues: 118.8424 Evaluate side-chains 100 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 0.1756 time to fit residues: 1.9483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0070 chunk 83 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 0.0030 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7585 Z= 0.216 Angle : 0.779 13.044 10306 Z= 0.357 Chirality : 0.041 0.335 1148 Planarity : 0.005 0.062 1337 Dihedral : 4.168 37.480 1035 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.15 % Allowed : 25.98 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.27), residues: 930 helix: 1.93 (0.21), residues: 621 sheet: -0.09 (0.88), residues: 35 loop : 0.71 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 441 HIS 0.004 0.001 HIS A 624 PHE 0.041 0.002 PHE A 465 TYR 0.030 0.002 TYR A 533 ARG 0.009 0.001 ARG A1007 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 0.8952 time to fit residues: 105.5400 Evaluate side-chains 97 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.2198 time to fit residues: 1.5515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.0070 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 73 optimal weight: 0.0170 chunk 7 optimal weight: 0.0010 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.0770 overall best weight: 0.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 274 GLN ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7585 Z= 0.221 Angle : 0.807 13.853 10306 Z= 0.370 Chirality : 0.041 0.337 1148 Planarity : 0.005 0.058 1337 Dihedral : 4.203 37.764 1035 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.65 % Allowed : 27.12 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.27), residues: 930 helix: 1.88 (0.21), residues: 621 sheet: 0.02 (0.91), residues: 35 loop : 0.67 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 441 HIS 0.004 0.001 HIS A 243 PHE 0.024 0.002 PHE A 497 TYR 0.038 0.002 TYR A 533 ARG 0.011 0.001 ARG A 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.8551 time to fit residues: 96.7840 Evaluate side-chains 94 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.1076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 0.0060 chunk 4 optimal weight: 5.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.138042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.104818 restraints weight = 28537.929| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 4.67 r_work: 0.3605 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7585 Z= 0.312 Angle : 0.839 13.781 10306 Z= 0.398 Chirality : 0.045 0.326 1148 Planarity : 0.006 0.066 1337 Dihedral : 4.350 25.992 1035 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.90 % Allowed : 26.87 % Favored : 71.23 % 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: 1.77 (0.27), residues: 930 helix: 1.59 (0.21), residues: 620 sheet: 0.13 (0.91), residues: 33 loop : 0.56 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP A 441 HIS 0.007 0.001 HIS A1138 PHE 0.041 0.003 PHE A 465 TYR 0.020 0.002 TYR A 468 ARG 0.012 0.001 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3039.63 seconds wall clock time: 54 minutes 42.04 seconds (3282.04 seconds total)