Starting phenix.real_space_refine on Sat Mar 16 12:45:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/03_2024/7pzr_13736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/03_2024/7pzr_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_13736/03_2024/7pzr_13736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/03_2024/7pzr_13736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/03_2024/7pzr_13736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzr_13736/03_2024/7pzr_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-dev-5265/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: 8.02, per 1000 atoms: 1.08 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: 3.12 Conformation dependent library (CDL) restraints added in 2.8 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: 0.88 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: 2.44 Time building geometry restraints manager: 3.36 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: 0.380 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: 2.140 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 29.940 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.740 ------------------------------------------------------------------------------- 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 : 0.880 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 REVERT: A 395 THR cc_start: 0.8442 (m) cc_final: 0.8148 (p) REVERT: A 482 MET cc_start: 0.8007 (ttp) cc_final: 0.7771 (ttm) REVERT: A 495 GLU cc_start: 0.8442 (tp30) cc_final: 0.8220 (tm-30) REVERT: A 988 LYS cc_start: 0.7535 (mtpt) cc_final: 0.6980 (mptt) REVERT: A 992 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7195 (tm-30) REVERT: A 1038 LYS cc_start: 0.7461 (mtmt) cc_final: 0.7234 (mmpt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 1.2791 time to fit residues: 319.1327 Evaluate side-chains 126 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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: 0.9980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 704 ASN A 788 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7585 Z= 0.255 Angle : 0.728 11.525 10306 Z= 0.362 Chirality : 0.039 0.149 1148 Planarity : 0.006 0.076 1337 Dihedral : 4.160 42.117 1035 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.80 % Allowed : 16.60 % Favored : 79.59 % 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: 2.87 (0.26), residues: 930 helix: 2.51 (0.19), residues: 638 sheet: 0.28 (0.83), residues: 33 loop : 0.65 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A1154 HIS 0.010 0.002 HIS A 920 PHE 0.051 0.003 PHE A 802 TYR 0.014 0.002 TYR A1031 ARG 0.009 0.001 ARG A 936 *********************** 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 161 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 MET cc_start: 0.7608 (mmp) cc_final: 0.7378 (mmp) REVERT: A 425 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8462 (pptt) REVERT: A 450 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7745 (mmm160) REVERT: A 495 GLU cc_start: 0.8574 (tp30) cc_final: 0.8277 (tm-30) REVERT: A 669 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8030 (pttt) REVERT: A 772 MET cc_start: 0.6936 (tmm) cc_final: 0.6358 (tmm) REVERT: A 822 ARG cc_start: 0.7143 (mtt90) cc_final: 0.6929 (mtt-85) REVERT: A 972 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: A 975 MET cc_start: 0.7241 (mmm) cc_final: 0.6676 (ttt) REVERT: A 977 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8950 (m) REVERT: A 992 GLN cc_start: 0.7546 (tp-100) cc_final: 0.7016 (tm-30) REVERT: A 1062 SER cc_start: 0.8850 (m) cc_final: 0.8375 (p) outliers start: 30 outliers final: 10 residues processed: 148 average time/residue: 0.9909 time to fit residues: 156.7358 Evaluate side-chains 109 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 972 GLN Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1230 SER 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: 3.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 HIS A 815 HIS A 921 GLN A1009 GLN A1035 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN A1170 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7585 Z= 0.283 Angle : 0.729 12.450 10306 Z= 0.354 Chirality : 0.040 0.141 1148 Planarity : 0.005 0.046 1337 Dihedral : 4.150 28.871 1035 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.31 % Allowed : 18.88 % Favored : 76.81 % 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: 2.45 (0.27), residues: 930 helix: 2.18 (0.20), residues: 621 sheet: -0.09 (0.86), residues: 35 loop : 0.69 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A1154 HIS 0.007 0.001 HIS A 920 PHE 0.032 0.003 PHE A 802 TYR 0.017 0.002 TYR A 468 ARG 0.008 0.001 ARG A 447 *********************** 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 147 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.8446 (tttt) cc_final: 0.8171 (tttt) REVERT: A 263 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7726 (ptm) REVERT: A 321 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: A 372 LYS cc_start: 0.7719 (pmtt) cc_final: 0.7489 (tptp) REVERT: A 495 GLU cc_start: 0.8710 (tp30) cc_final: 0.8273 (tm-30) REVERT: A 669 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7961 (pttt) REVERT: A 868 MET cc_start: 0.6930 (tmm) cc_final: 0.6164 (tpp) REVERT: A 975 MET cc_start: 0.7320 (mmm) cc_final: 0.6823 (ttt) REVERT: A 1062 SER cc_start: 0.8917 (m) cc_final: 0.8426 (p) outliers start: 34 outliers final: 15 residues processed: 131 average time/residue: 1.0438 time to fit residues: 145.8495 Evaluate side-chains 107 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1230 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 GLN A1164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7585 Z= 0.224 Angle : 0.735 14.583 10306 Z= 0.347 Chirality : 0.039 0.205 1148 Planarity : 0.005 0.071 1337 Dihedral : 4.096 30.732 1035 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.30 % Allowed : 21.17 % Favored : 75.54 % 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: 2.14 (0.20), residues: 621 sheet: 0.02 (0.87), residues: 35 loop : 0.76 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1154 HIS 0.005 0.001 HIS A 624 PHE 0.033 0.002 PHE A 465 TYR 0.013 0.001 TYR A 468 ARG 0.011 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 130 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7261 (ptm) REVERT: A 286 MET cc_start: 0.7693 (mmp) cc_final: 0.7481 (tpp) REVERT: A 321 GLU cc_start: 0.7847 (pt0) cc_final: 0.7524 (pp20) REVERT: A 495 GLU cc_start: 0.8701 (tp30) cc_final: 0.8263 (tm-30) REVERT: A 566 PRO cc_start: 0.7757 (Cg_endo) cc_final: 0.7502 (Cg_exo) REVERT: A 669 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7947 (pttt) REVERT: A 772 MET cc_start: 0.7024 (tmm) cc_final: 0.6562 (tmm) REVERT: A 868 MET cc_start: 0.6931 (tmm) cc_final: 0.6317 (tpp) REVERT: A 975 MET cc_start: 0.7487 (mmm) cc_final: 0.6902 (ttm) REVERT: A 1062 SER cc_start: 0.8920 (m) cc_final: 0.8416 (p) outliers start: 26 outliers final: 13 residues processed: 119 average time/residue: 0.9953 time to fit residues: 126.7678 Evaluate side-chains 105 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1230 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 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 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 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: 0.7186 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7585 Z= 0.230 Angle : 0.734 14.138 10306 Z= 0.342 Chirality : 0.040 0.375 1148 Planarity : 0.005 0.041 1337 Dihedral : 4.115 28.227 1035 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.93 % Allowed : 20.66 % Favored : 75.41 % 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: 1.99 (0.21), residues: 620 sheet: 0.05 (0.88), residues: 35 loop : 0.75 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1154 HIS 0.005 0.001 HIS A 624 PHE 0.032 0.003 PHE A 277 TYR 0.030 0.002 TYR A 533 ARG 0.009 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 132 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 286 MET cc_start: 0.7707 (mmp) cc_final: 0.7492 (tpp) REVERT: A 321 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7542 (pp20) REVERT: A 451 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8681 (mm-30) REVERT: A 495 GLU cc_start: 0.8698 (tp30) cc_final: 0.8249 (tm-30) REVERT: A 669 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7955 (pttt) REVERT: A 772 MET cc_start: 0.7098 (tmm) cc_final: 0.6522 (tmm) REVERT: A 868 MET cc_start: 0.6924 (tmm) cc_final: 0.6384 (tpp) REVERT: A 972 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: A 987 ARG cc_start: 0.7069 (ttt-90) cc_final: 0.6810 (ttt180) REVERT: A 992 GLN cc_start: 0.7551 (tp-100) cc_final: 0.7296 (tm-30) REVERT: A 1010 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7990 (tp) REVERT: A 1062 SER cc_start: 0.8944 (m) cc_final: 0.8465 (p) REVERT: A 1219 LEU cc_start: 0.7969 (tp) cc_final: 0.7768 (mt) outliers start: 31 outliers final: 12 residues processed: 121 average time/residue: 0.9773 time to fit residues: 126.9412 Evaluate side-chains 111 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 972 GLN Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1230 SER 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: 5.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 680 HIS A1164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7585 Z= 0.235 Angle : 0.758 13.831 10306 Z= 0.353 Chirality : 0.040 0.359 1148 Planarity : 0.005 0.088 1337 Dihedral : 4.074 27.920 1035 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.80 % Allowed : 22.18 % Favored : 74.02 % 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: 1.98 (0.21), residues: 620 sheet: 0.14 (0.90), residues: 35 loop : 0.79 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1154 HIS 0.004 0.001 HIS A 624 PHE 0.032 0.002 PHE A 465 TYR 0.031 0.002 TYR A 533 ARG 0.007 0.001 ARG A 976 *********************** 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 130 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7330 (ptm) REVERT: A 277 PHE cc_start: 0.7465 (t80) cc_final: 0.6717 (t80) REVERT: A 321 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7548 (pp20) REVERT: A 441 TRP cc_start: 0.7681 (m-10) cc_final: 0.7195 (m-90) REVERT: A 451 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8673 (mm-30) REVERT: A 495 GLU cc_start: 0.8735 (tp30) cc_final: 0.8334 (tm-30) REVERT: A 573 MET cc_start: 0.7798 (mmm) cc_final: 0.7254 (mmm) REVERT: A 669 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8015 (pttt) REVERT: A 868 MET cc_start: 0.6902 (tmm) cc_final: 0.6379 (tpp) REVERT: A 975 MET cc_start: 0.7233 (mmm) cc_final: 0.6823 (ttt) REVERT: A 992 GLN cc_start: 0.7804 (tp-100) cc_final: 0.7387 (tm-30) REVERT: A 1062 SER cc_start: 0.8906 (m) cc_final: 0.8421 (p) REVERT: A 1219 LEU cc_start: 0.8004 (tp) cc_final: 0.7803 (mt) outliers start: 30 outliers final: 14 residues processed: 119 average time/residue: 0.9084 time to fit residues: 116.4037 Evaluate side-chains 108 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1230 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 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: 0.7175 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7585 Z= 0.217 Angle : 0.758 13.592 10306 Z= 0.352 Chirality : 0.040 0.265 1148 Planarity : 0.005 0.072 1337 Dihedral : 4.060 30.365 1035 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.30 % Allowed : 23.83 % Favored : 72.88 % 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 (0.28), residues: 930 helix: 2.00 (0.21), residues: 621 sheet: -0.09 (0.87), residues: 35 loop : 0.78 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1154 HIS 0.004 0.001 HIS A 624 PHE 0.037 0.002 PHE A 465 TYR 0.034 0.002 TYR A 533 ARG 0.008 0.001 ARG A 976 *********************** 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 125 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7539 (ptm) REVERT: A 321 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7512 (pp20) REVERT: A 432 LYS cc_start: 0.9077 (ptmt) cc_final: 0.8874 (pttm) REVERT: A 441 TRP cc_start: 0.7776 (m-10) cc_final: 0.7258 (m-90) REVERT: A 451 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8680 (mm-30) REVERT: A 495 GLU cc_start: 0.8775 (tp30) cc_final: 0.8134 (tm-30) REVERT: A 573 MET cc_start: 0.7752 (mmm) cc_final: 0.7245 (mmm) REVERT: A 669 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8053 (pttt) REVERT: A 868 MET cc_start: 0.6789 (tmm) cc_final: 0.6380 (tpp) REVERT: A 972 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: A 975 MET cc_start: 0.7156 (mmm) cc_final: 0.6703 (ttt) REVERT: A 992 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7357 (tm-30) REVERT: A 1062 SER cc_start: 0.8998 (m) cc_final: 0.8518 (p) REVERT: A 1219 LEU cc_start: 0.7923 (tp) cc_final: 0.7714 (mt) outliers start: 26 outliers final: 12 residues processed: 117 average time/residue: 0.9775 time to fit residues: 122.7110 Evaluate side-chains 107 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 972 GLN Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1230 SER 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: 2.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 70 optimal weight: 0.0270 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- 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** A1164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7585 Z= 0.226 Angle : 0.756 13.628 10306 Z= 0.354 Chirality : 0.040 0.328 1148 Planarity : 0.005 0.063 1337 Dihedral : 4.064 29.852 1035 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.92 % Allowed : 24.46 % Favored : 72.62 % 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 (0.28), residues: 930 helix: 1.96 (0.21), residues: 621 sheet: 0.41 (0.94), residues: 33 loop : 0.78 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1154 HIS 0.005 0.001 HIS A 624 PHE 0.039 0.002 PHE A 465 TYR 0.013 0.001 TYR A 530 ARG 0.007 0.001 ARG A 976 *********************** 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 119 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7345 (ptm) REVERT: A 321 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7521 (pp20) REVERT: A 441 TRP cc_start: 0.7761 (m-10) cc_final: 0.7235 (m-90) REVERT: A 451 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8640 (mm-30) REVERT: A 495 GLU cc_start: 0.8789 (tp30) cc_final: 0.8311 (tm-30) REVERT: A 573 MET cc_start: 0.7755 (mmm) cc_final: 0.7164 (mmm) REVERT: A 669 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7989 (pmtt) REVERT: A 868 MET cc_start: 0.6824 (tmm) cc_final: 0.6444 (tpp) REVERT: A 975 MET cc_start: 0.7206 (mmm) cc_final: 0.6706 (ttt) REVERT: A 1062 SER cc_start: 0.9017 (m) cc_final: 0.8527 (p) outliers start: 23 outliers final: 14 residues processed: 113 average time/residue: 0.9588 time to fit residues: 116.3441 Evaluate side-chains 108 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1230 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 0.0670 chunk 88 optimal weight: 0.7980 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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** A1164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.5765 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 : 0.767 13.664 10306 Z= 0.359 Chirality : 0.040 0.321 1148 Planarity : 0.005 0.058 1337 Dihedral : 4.081 31.722 1035 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.04 % Allowed : 24.71 % 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: 2.25 (0.28), residues: 930 helix: 1.96 (0.21), residues: 621 sheet: 0.03 (0.92), residues: 35 loop : 0.75 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1026 HIS 0.006 0.001 HIS A 250 PHE 0.042 0.002 PHE A 465 TYR 0.023 0.002 TYR A 468 ARG 0.013 0.001 ARG A 481 *********************** 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 121 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7185 (ptm) REVERT: A 321 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7512 (pp20) REVERT: A 441 TRP cc_start: 0.7776 (m-10) cc_final: 0.7248 (m-90) REVERT: A 451 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8648 (mm-30) REVERT: A 495 GLU cc_start: 0.8790 (tp30) cc_final: 0.8356 (tm-30) REVERT: A 573 MET cc_start: 0.7712 (mmm) cc_final: 0.7117 (mmm) REVERT: A 669 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8004 (pmtt) REVERT: A 868 MET cc_start: 0.7017 (tmm) cc_final: 0.6639 (tpp) REVERT: A 975 MET cc_start: 0.7295 (mmm) cc_final: 0.6587 (ttt) REVERT: A 1062 SER cc_start: 0.8998 (m) cc_final: 0.8503 (p) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.8575 time to fit residues: 104.0734 Evaluate side-chains 106 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1029 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 0.0010 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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** A1164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.5873 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= 0.215 Angle : 0.774 13.330 10306 Z= 0.363 Chirality : 0.041 0.319 1148 Planarity : 0.005 0.068 1337 Dihedral : 4.135 32.986 1035 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.28 % Allowed : 25.48 % 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: 2.25 (0.28), residues: 930 helix: 1.98 (0.21), residues: 621 sheet: 0.14 (0.97), residues: 33 loop : 0.69 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1026 HIS 0.005 0.001 HIS A 250 PHE 0.027 0.002 PHE A 497 TYR 0.022 0.001 TYR A 468 ARG 0.012 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 113 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7507 (pp20) REVERT: A 441 TRP cc_start: 0.7859 (m-10) cc_final: 0.7311 (m-90) REVERT: A 451 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8648 (mm-30) REVERT: A 495 GLU cc_start: 0.8805 (tp30) cc_final: 0.8282 (tm-30) REVERT: A 573 MET cc_start: 0.7701 (mmm) cc_final: 0.7117 (mmm) REVERT: A 669 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8017 (pmtt) REVERT: A 868 MET cc_start: 0.7006 (tmm) cc_final: 0.6657 (tpp) REVERT: A 975 MET cc_start: 0.7231 (mmm) cc_final: 0.6469 (ttt) REVERT: A 1062 SER cc_start: 0.8988 (m) cc_final: 0.8493 (p) outliers start: 18 outliers final: 12 residues processed: 109 average time/residue: 0.8528 time to fit residues: 100.5393 Evaluate side-chains 102 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 972 GLN Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1029 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.141292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.108700 restraints weight = 28656.041| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 4.93 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7585 Z= 0.226 Angle : 0.780 13.121 10306 Z= 0.367 Chirality : 0.041 0.319 1148 Planarity : 0.006 0.064 1337 Dihedral : 4.163 32.973 1035 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.15 % Allowed : 25.73 % Favored : 72.12 % 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: 2.17 (0.27), residues: 930 helix: 1.93 (0.21), residues: 621 sheet: 0.15 (0.97), residues: 33 loop : 0.64 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1026 HIS 0.006 0.001 HIS A 250 PHE 0.040 0.002 PHE A 465 TYR 0.029 0.002 TYR A 533 ARG 0.014 0.001 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.14 seconds wall clock time: 52 minutes 45.51 seconds (3165.51 seconds total)