Starting phenix.real_space_refine on Fri Jul 25 20:10:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qpv_53284/07_2025/9qpv_53284.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qpv_53284/07_2025/9qpv_53284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qpv_53284/07_2025/9qpv_53284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qpv_53284/07_2025/9qpv_53284.map" model { file = "/net/cci-nas-00/data/ceres_data/9qpv_53284/07_2025/9qpv_53284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qpv_53284/07_2025/9qpv_53284.cif" } resolution = 3.3 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= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 4912 2.51 5 N 1413 2.21 5 O 1433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7776 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7776 Classifications: {'peptide': 1000} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 943} Chain breaks: 4 Time building chain proxies: 5.08, per 1000 atoms: 0.65 Number of scatterers: 7776 At special positions: 0 Unit cell: (63, 107.52, 133.56, 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 18 16.00 O 1433 8.00 N 1413 7.00 C 4912 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 - 3.00 Amino acid : True - 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: 2.10 Conformation dependent library (CDL) restraints added in 957.0 milliseconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1858 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 58.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 removed outlier: 4.248A pdb=" N ALA A 55 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.689A pdb=" N VAL A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.547A pdb=" N HIS A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.903A pdb=" N ARG A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 243 through 244 No H-bonds generated for 'chain 'A' and resid 243 through 244' Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 259 through 284 Processing helix chain 'A' and resid 289 through 311 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 421 through 452 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 491 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 512 through 516 removed outlier: 3.871A pdb=" N LEU A 516 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.692A pdb=" N ALA A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 541 through 554 Processing helix chain 'A' and resid 564 through 578 removed outlier: 3.881A pdb=" N LEU A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 599 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.593A pdb=" N GLY A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A 622 " --> pdb=" O GLY A 618 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 671 Processing helix chain 'A' and resid 674 through 703 removed outlier: 3.692A pdb=" N ARG A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 746 Processing helix chain 'A' and resid 758 through 784 Processing helix chain 'A' and resid 786 through 831 removed outlier: 3.753A pdb=" N MET A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) Proline residue: A 792 - end of helix removed outlier: 4.025A pdb=" N VAL A 821 " --> pdb=" O GLN A 817 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 850 through 860 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 877 through 890 Processing helix chain 'A' and resid 909 through 914 Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 929 through 940 removed outlier: 3.660A pdb=" N PHE A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 950 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 985 through 998 Processing helix chain 'A' and resid 1033 through 1038 Processing helix chain 'A' and resid 1073 through 1081 removed outlier: 3.717A pdb=" N VAL A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1165 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 removed outlier: 4.213A pdb=" N LEU A 122 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 71 removed outlier: 6.616A pdb=" N GLN A 39 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU A 255 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 41 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.454A pdb=" N ARG A 92 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU A 101 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU A 90 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 630 through 633 Processing sheet with id=AA5, first strand: chain 'A' and resid 1092 through 1093 removed outlier: 4.459A pdb=" N ILE A1025 " --> pdb=" O VAL A1093 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A1022 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1067 through 1072 removed outlier: 3.553A pdb=" N ILE A1117 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A1119 " --> pdb=" O HIS A1127 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A1127 " --> pdb=" O ARG A1119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1067 through 1072 465 hydrogen bonds defined for protein. 1311 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: 2.71 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2670 1.34 - 1.46: 1222 1.46 - 1.57: 4012 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 7936 Sorted by residual: bond pdb=" CB VAL A 849 " pdb=" CG2 VAL A 849 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.35e+00 bond pdb=" N ARG A 66 " pdb=" CA ARG A 66 " ideal model delta sigma weight residual 1.455 1.439 0.016 1.61e-02 3.86e+03 9.98e-01 bond pdb=" CG GLN A 769 " pdb=" CD GLN A 769 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.60e-01 bond pdb=" CB VAL A1133 " pdb=" CG2 VAL A1133 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.41e-01 bond pdb=" C ARG A 938 " pdb=" N PHE A 939 " ideal model delta sigma weight residual 1.324 1.346 -0.022 2.56e-02 1.53e+03 7.29e-01 ... (remaining 7931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 10567 2.21 - 4.42: 182 4.42 - 6.64: 32 6.64 - 8.85: 2 8.85 - 11.06: 1 Bond angle restraints: 10784 Sorted by residual: angle pdb=" C VAL A1090 " pdb=" N LEU A1091 " pdb=" CA LEU A1091 " ideal model delta sigma weight residual 121.75 127.52 -5.77 1.73e+00 3.34e-01 1.11e+01 angle pdb=" N ASN A 579 " pdb=" CA ASN A 579 " pdb=" C ASN A 579 " ideal model delta sigma weight residual 109.81 117.14 -7.33 2.21e+00 2.05e-01 1.10e+01 angle pdb=" CA LEU A 642 " pdb=" CB LEU A 642 " pdb=" CG LEU A 642 " ideal model delta sigma weight residual 116.30 105.24 11.06 3.50e+00 8.16e-02 9.99e+00 angle pdb=" C LEU A1089 " pdb=" N VAL A1090 " pdb=" CA VAL A1090 " ideal model delta sigma weight residual 122.58 118.22 4.36 1.48e+00 4.57e-01 8.68e+00 angle pdb=" N LEU A1089 " pdb=" CA LEU A1089 " pdb=" C LEU A1089 " ideal model delta sigma weight residual 112.03 115.88 -3.85 1.31e+00 5.83e-01 8.63e+00 ... (remaining 10779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 4362 16.35 - 32.69: 363 32.69 - 49.04: 49 49.04 - 65.39: 20 65.39 - 81.73: 9 Dihedral angle restraints: 4803 sinusoidal: 1923 harmonic: 2880 Sorted by residual: dihedral pdb=" CA THR A 455 " pdb=" C THR A 455 " pdb=" N GLU A 456 " pdb=" CA GLU A 456 " ideal model delta harmonic sigma weight residual 180.00 150.52 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA THR A 515 " pdb=" C THR A 515 " pdb=" N LEU A 516 " pdb=" CA LEU A 516 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ASN A 75 " pdb=" C ASN A 75 " pdb=" N GLY A 76 " pdb=" CA GLY A 76 " ideal model delta harmonic sigma weight residual 180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 4800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 834 0.042 - 0.085: 267 0.085 - 0.127: 78 0.127 - 0.169: 18 0.169 - 0.212: 3 Chirality restraints: 1200 Sorted by residual: chirality pdb=" CG LEU A 176 " pdb=" CB LEU A 176 " pdb=" CD1 LEU A 176 " pdb=" CD2 LEU A 176 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU A 436 " pdb=" CB LEU A 436 " pdb=" CD1 LEU A 436 " pdb=" CD2 LEU A 436 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA ASN A 579 " pdb=" N ASN A 579 " pdb=" C ASN A 579 " pdb=" CB ASN A 579 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 1197 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 466 " -0.009 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" CG TYR A 466 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 466 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 466 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 466 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 466 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 466 " 0.037 2.00e-02 2.50e+03 pdb=" OH TYR A 466 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 66 " -0.213 9.50e-02 1.11e+02 9.64e-02 7.39e+00 pdb=" NE ARG A 66 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 66 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 66 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 66 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 493 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C GLU A 493 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU A 493 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 494 " 0.016 2.00e-02 2.50e+03 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 524 2.74 - 3.28: 8483 3.28 - 3.82: 13267 3.82 - 4.36: 16460 4.36 - 4.90: 27188 Nonbonded interactions: 65922 Sorted by model distance: nonbonded pdb=" O LEU A 982 " pdb=" OH TYR A 989 " model vdw 2.194 3.040 nonbonded pdb=" OE1 GLN A 863 " pdb=" NH2 ARG A 938 " model vdw 2.234 3.120 nonbonded pdb=" O SER A 796 " pdb=" OG1 THR A 799 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR A 907 " pdb=" O ARG A1044 " model vdw 2.279 3.040 nonbonded pdb=" OE1 GLN A 190 " pdb=" OH TYR A 224 " model vdw 2.291 3.040 ... (remaining 65917 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=0.00 max=1.00 mean=1.00 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 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 : 0.003 0.038 7936 Z= 0.160 Angle : 0.758 11.062 10784 Z= 0.429 Chirality : 0.047 0.212 1200 Planarity : 0.010 0.096 1425 Dihedral : 13.050 81.731 2945 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 (0.24), residues: 990 helix: -1.48 (0.19), residues: 516 sheet: -0.56 (0.51), residues: 106 loop : -1.60 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 925 HIS 0.003 0.001 HIS A1138 PHE 0.019 0.003 PHE A 61 TYR 0.042 0.006 TYR A 466 ARG 0.023 0.003 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.14031 ( 445) hydrogen bonds : angle 7.47294 ( 1311) covalent geometry : bond 0.00325 ( 7936) covalent geometry : angle 0.75838 (10784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.775 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8014 (mmm160) cc_final: 0.7781 (mmm-85) REVERT: A 630 THR cc_start: 0.7554 (m) cc_final: 0.7243 (p) REVERT: A 874 ARG cc_start: 0.6501 (mtt180) cc_final: 0.5959 (ptp-170) REVERT: A 1132 MET cc_start: 0.6228 (mmt) cc_final: 0.5950 (tpp) REVERT: A 1165 LEU cc_start: 0.8537 (mp) cc_final: 0.8318 (mt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2645 time to fit residues: 82.1358 Evaluate side-chains 161 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.0270 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.148215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.118350 restraints weight = 14518.443| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.95 r_work: 0.3617 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7936 Z= 0.192 Angle : 0.785 9.730 10784 Z= 0.403 Chirality : 0.046 0.188 1200 Planarity : 0.006 0.059 1425 Dihedral : 6.173 27.853 1100 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.26 % Allowed : 10.44 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.26), residues: 990 helix: 0.08 (0.22), residues: 525 sheet: -0.75 (0.45), residues: 124 loop : -0.99 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 439 HIS 0.003 0.001 HIS A1131 PHE 0.035 0.003 PHE A 513 TYR 0.029 0.003 TYR A 45 ARG 0.009 0.001 ARG A1130 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 445) hydrogen bonds : angle 5.60031 ( 1311) covalent geometry : bond 0.00418 ( 7936) covalent geometry : angle 0.78545 (10784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.775 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: A 104 GLN cc_start: 0.7562 (pp30) cc_final: 0.7146 (pp30) REVERT: A 128 SER cc_start: 0.7060 (t) cc_final: 0.6819 (p) REVERT: A 293 ARG cc_start: 0.6678 (ttp-170) cc_final: 0.6300 (ptp-170) REVERT: A 308 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8071 (mmm-85) REVERT: A 417 ASP cc_start: 0.8191 (m-30) cc_final: 0.7601 (p0) REVERT: A 590 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7367 (mpp) REVERT: A 630 THR cc_start: 0.7791 (m) cc_final: 0.7326 (p) REVERT: A 658 ARG cc_start: 0.8472 (mtm110) cc_final: 0.8163 (mtm-85) REVERT: A 748 TYR cc_start: 0.7784 (m-80) cc_final: 0.7536 (m-80) REVERT: A 749 SER cc_start: 0.8695 (m) cc_final: 0.8485 (p) REVERT: A 874 ARG cc_start: 0.6792 (mtt180) cc_final: 0.6577 (mtt-85) REVERT: A 994 LEU cc_start: 0.8650 (mt) cc_final: 0.7995 (mp) REVERT: A 1027 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7946 (mp) REVERT: A 1081 LEU cc_start: 0.8420 (pt) cc_final: 0.8113 (pt) REVERT: A 1132 MET cc_start: 0.7865 (mmt) cc_final: 0.7441 (mmt) outliers start: 18 outliers final: 10 residues processed: 186 average time/residue: 0.2517 time to fit residues: 59.9438 Evaluate side-chains 158 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 989 TYR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1139 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS A 547 GLN A 662 GLN ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.145935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.116488 restraints weight = 14554.566| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.99 r_work: 0.3576 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7936 Z= 0.179 Angle : 0.743 9.728 10784 Z= 0.375 Chirality : 0.045 0.260 1200 Planarity : 0.006 0.064 1425 Dihedral : 5.634 27.384 1100 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.77 % Allowed : 12.08 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 990 helix: 0.39 (0.22), residues: 522 sheet: -0.70 (0.44), residues: 126 loop : -0.79 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 956 HIS 0.003 0.001 HIS A 843 PHE 0.020 0.002 PHE A 513 TYR 0.024 0.002 TYR A 248 ARG 0.007 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 445) hydrogen bonds : angle 5.28859 ( 1311) covalent geometry : bond 0.00376 ( 7936) covalent geometry : angle 0.74296 (10784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.7777 (p90) cc_final: 0.7520 (p90) REVERT: A 104 GLN cc_start: 0.7545 (pp30) cc_final: 0.7217 (pp30) REVERT: A 145 MET cc_start: 0.7101 (mmm) cc_final: 0.6867 (mmt) REVERT: A 164 ARG cc_start: 0.8727 (ttm-80) cc_final: 0.8427 (ttm-80) REVERT: A 293 ARG cc_start: 0.6720 (ttp-170) cc_final: 0.6392 (ttp-110) REVERT: A 308 ARG cc_start: 0.8524 (mmm160) cc_final: 0.8051 (mmm-85) REVERT: A 527 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8519 (mt0) REVERT: A 590 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7549 (mpp) REVERT: A 593 PHE cc_start: 0.8360 (t80) cc_final: 0.8153 (t80) REVERT: A 638 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 749 SER cc_start: 0.8786 (m) cc_final: 0.8564 (p) REVERT: A 869 TRP cc_start: 0.7861 (t60) cc_final: 0.7508 (t60) REVERT: A 957 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5050 (m-80) REVERT: A 1001 ARG cc_start: 0.7532 (ttt90) cc_final: 0.7311 (ttt90) REVERT: A 1027 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 1081 LEU cc_start: 0.8367 (pt) cc_final: 0.8137 (pt) REVERT: A 1132 MET cc_start: 0.8012 (mmt) cc_final: 0.7553 (mmt) outliers start: 22 outliers final: 12 residues processed: 169 average time/residue: 0.2601 time to fit residues: 56.6669 Evaluate side-chains 153 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 957 TYR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1139 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 198 GLN A 201 GLN A 662 GLN A 825 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.150483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.123933 restraints weight = 14517.185| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 3.53 r_work: 0.3761 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7936 Z= 0.209 Angle : 0.741 9.159 10784 Z= 0.376 Chirality : 0.046 0.186 1200 Planarity : 0.006 0.063 1425 Dihedral : 5.401 25.379 1100 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.40 % Allowed : 13.08 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 990 helix: 0.50 (0.22), residues: 515 sheet: -0.74 (0.44), residues: 126 loop : -0.79 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 956 HIS 0.004 0.001 HIS A 536 PHE 0.023 0.003 PHE A 848 TYR 0.023 0.002 TYR A 248 ARG 0.006 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 445) hydrogen bonds : angle 5.26278 ( 1311) covalent geometry : bond 0.00462 ( 7936) covalent geometry : angle 0.74092 (10784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7472 (pp30) cc_final: 0.7152 (pp30) REVERT: A 145 MET cc_start: 0.7242 (mmm) cc_final: 0.6982 (mmt) REVERT: A 308 ARG cc_start: 0.8358 (mmm160) cc_final: 0.7949 (mmm-85) REVERT: A 527 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8631 (mt0) REVERT: A 590 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7813 (mpp) REVERT: A 661 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8487 (tmm160) REVERT: A 662 GLN cc_start: 0.8825 (pt0) cc_final: 0.7998 (pt0) REVERT: A 745 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6931 (mtp-110) REVERT: A 957 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.5257 (m-80) REVERT: A 1027 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8040 (mp) REVERT: A 1132 MET cc_start: 0.8051 (mmt) cc_final: 0.7606 (mmt) outliers start: 27 outliers final: 14 residues processed: 158 average time/residue: 0.2383 time to fit residues: 49.0068 Evaluate side-chains 143 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 957 TYR Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1139 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.0870 chunk 88 optimal weight: 10.0000 chunk 65 optimal weight: 0.1980 chunk 71 optimal weight: 0.5980 chunk 93 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 772 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.151083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.124400 restraints weight = 14402.890| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 3.61 r_work: 0.3799 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7936 Z= 0.172 Angle : 0.728 9.593 10784 Z= 0.365 Chirality : 0.046 0.219 1200 Planarity : 0.006 0.064 1425 Dihedral : 5.300 24.887 1100 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.89 % Allowed : 13.58 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 990 helix: 0.61 (0.22), residues: 514 sheet: -0.72 (0.44), residues: 126 loop : -0.85 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 869 HIS 0.003 0.001 HIS A 460 PHE 0.029 0.003 PHE A 798 TYR 0.018 0.002 TYR A 248 ARG 0.013 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 445) hydrogen bonds : angle 5.25279 ( 1311) covalent geometry : bond 0.00386 ( 7936) covalent geometry : angle 0.72833 (10784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7476 (mm) cc_final: 0.7254 (mm) REVERT: A 104 GLN cc_start: 0.7449 (pp30) cc_final: 0.7114 (pp30) REVERT: A 145 MET cc_start: 0.7204 (mmm) cc_final: 0.6979 (mmt) REVERT: A 308 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7923 (mmm-85) REVERT: A 590 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7975 (mpp) REVERT: A 661 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8332 (ttp80) REVERT: A 662 GLN cc_start: 0.8947 (pt0) cc_final: 0.8739 (pt0) REVERT: A 745 ARG cc_start: 0.7254 (mtp180) cc_final: 0.7046 (mtp180) REVERT: A 957 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5547 (m-80) REVERT: A 966 ASP cc_start: 0.8604 (m-30) cc_final: 0.8348 (t0) REVERT: A 1027 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7998 (mp) REVERT: A 1132 MET cc_start: 0.8045 (mmt) cc_final: 0.7454 (mmt) outliers start: 23 outliers final: 13 residues processed: 153 average time/residue: 0.3028 time to fit residues: 59.6536 Evaluate side-chains 132 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 957 TYR Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1160 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 47 optimal weight: 0.0040 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.153011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.124523 restraints weight = 14727.322| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 3.82 r_work: 0.3799 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7936 Z= 0.156 Angle : 0.726 10.136 10784 Z= 0.360 Chirality : 0.044 0.250 1200 Planarity : 0.005 0.063 1425 Dihedral : 5.167 22.907 1100 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.77 % Allowed : 15.35 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 990 helix: 0.76 (0.23), residues: 509 sheet: -0.62 (0.45), residues: 116 loop : -1.03 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 869 HIS 0.002 0.001 HIS A 830 PHE 0.024 0.003 PHE A 798 TYR 0.043 0.002 TYR A 45 ARG 0.006 0.001 ARG A1163 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 445) hydrogen bonds : angle 5.13184 ( 1311) covalent geometry : bond 0.00338 ( 7936) covalent geometry : angle 0.72588 (10784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7461 (pp30) cc_final: 0.7119 (pp30) REVERT: A 308 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7998 (mmm-85) REVERT: A 311 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8226 (mm-30) REVERT: A 590 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8156 (mpp) REVERT: A 661 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8429 (tmm160) REVERT: A 662 GLN cc_start: 0.9008 (pt0) cc_final: 0.8127 (pt0) REVERT: A 745 ARG cc_start: 0.7249 (mtp180) cc_final: 0.6995 (mtp-110) REVERT: A 957 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: A 1001 ARG cc_start: 0.7442 (ttt90) cc_final: 0.7152 (ttm-80) REVERT: A 1119 ARG cc_start: 0.8364 (mmt90) cc_final: 0.8007 (mmt90) REVERT: A 1132 MET cc_start: 0.8068 (mmt) cc_final: 0.7697 (tpp) outliers start: 22 outliers final: 12 residues processed: 144 average time/residue: 0.3435 time to fit residues: 64.2903 Evaluate side-chains 128 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 957 TYR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1160 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 198 GLN A 457 GLN A 521 GLN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.149307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119166 restraints weight = 14831.660| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.84 r_work: 0.3684 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.7498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7936 Z= 0.247 Angle : 0.794 11.477 10784 Z= 0.401 Chirality : 0.048 0.292 1200 Planarity : 0.006 0.061 1425 Dihedral : 5.354 23.655 1100 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.39 % Allowed : 15.85 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 990 helix: 0.40 (0.22), residues: 510 sheet: -0.99 (0.43), residues: 124 loop : -1.04 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 968 HIS 0.004 0.001 HIS A 843 PHE 0.054 0.004 PHE A 798 TYR 0.020 0.002 TYR A 134 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.05220 ( 445) hydrogen bonds : angle 5.36663 ( 1311) covalent geometry : bond 0.00539 ( 7936) covalent geometry : angle 0.79366 (10784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7618 (pp30) cc_final: 0.7194 (pp30) REVERT: A 248 TYR cc_start: 0.6239 (t80) cc_final: 0.5412 (t80) REVERT: A 251 ASP cc_start: 0.8280 (m-30) cc_final: 0.7688 (p0) REVERT: A 308 ARG cc_start: 0.8472 (mmm160) cc_final: 0.8035 (mmm-85) REVERT: A 661 ARG cc_start: 0.8753 (ttp80) cc_final: 0.8483 (tmm160) REVERT: A 662 GLN cc_start: 0.9091 (pt0) cc_final: 0.8264 (pt0) REVERT: A 745 ARG cc_start: 0.7538 (mtp180) cc_final: 0.7070 (mtp85) REVERT: A 957 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.6028 (m-80) REVERT: A 1001 ARG cc_start: 0.7578 (ttt90) cc_final: 0.7124 (ttm-80) REVERT: A 1132 MET cc_start: 0.7897 (mmt) cc_final: 0.7503 (tpp) outliers start: 19 outliers final: 10 residues processed: 139 average time/residue: 0.2695 time to fit residues: 48.8180 Evaluate side-chains 128 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 957 TYR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1160 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 0.0470 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 40 optimal weight: 0.3980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.155184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.125835 restraints weight = 14832.449| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.86 r_work: 0.3774 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.7819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7936 Z= 0.154 Angle : 0.760 11.764 10784 Z= 0.373 Chirality : 0.046 0.283 1200 Planarity : 0.006 0.064 1425 Dihedral : 5.216 23.543 1100 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.89 % Allowed : 17.36 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 990 helix: 0.71 (0.23), residues: 509 sheet: -0.66 (0.46), residues: 113 loop : -1.11 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 968 HIS 0.004 0.001 HIS A 460 PHE 0.047 0.003 PHE A 798 TYR 0.020 0.002 TYR A 134 ARG 0.009 0.001 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 445) hydrogen bonds : angle 5.24282 ( 1311) covalent geometry : bond 0.00338 ( 7936) covalent geometry : angle 0.76011 (10784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7548 (pp30) cc_final: 0.7141 (pp30) REVERT: A 179 ARG cc_start: 0.8228 (ttp80) cc_final: 0.8018 (tpt90) REVERT: A 251 ASP cc_start: 0.8221 (m-30) cc_final: 0.7293 (t0) REVERT: A 308 ARG cc_start: 0.8362 (mmm160) cc_final: 0.7977 (mmm-85) REVERT: A 527 GLN cc_start: 0.8712 (mt0) cc_final: 0.8466 (pt0) REVERT: A 661 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8391 (tmm160) REVERT: A 662 GLN cc_start: 0.9077 (pt0) cc_final: 0.8195 (pt0) REVERT: A 745 ARG cc_start: 0.7440 (mtp180) cc_final: 0.7162 (mtp85) REVERT: A 809 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6589 (tp40) REVERT: A 951 LEU cc_start: 0.8550 (mm) cc_final: 0.7919 (mm) REVERT: A 957 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: A 1001 ARG cc_start: 0.7389 (ttt90) cc_final: 0.6995 (ttm-80) REVERT: A 1132 MET cc_start: 0.7798 (mmt) cc_final: 0.7513 (tpp) outliers start: 15 outliers final: 10 residues processed: 133 average time/residue: 0.2599 time to fit residues: 45.4457 Evaluate side-chains 123 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 957 TYR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1139 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.148263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.120718 restraints weight = 14757.696| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.68 r_work: 0.3746 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.8092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7936 Z= 0.187 Angle : 0.778 13.974 10784 Z= 0.384 Chirality : 0.049 0.267 1200 Planarity : 0.006 0.081 1425 Dihedral : 5.187 21.481 1100 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.01 % Allowed : 17.86 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.27), residues: 990 helix: 0.69 (0.23), residues: 505 sheet: -0.26 (0.49), residues: 96 loop : -1.19 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 968 HIS 0.004 0.001 HIS A 460 PHE 0.046 0.004 PHE A 798 TYR 0.021 0.002 TYR A 134 ARG 0.009 0.001 ARG A 258 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 445) hydrogen bonds : angle 5.36496 ( 1311) covalent geometry : bond 0.00421 ( 7936) covalent geometry : angle 0.77780 (10784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7494 (pp30) cc_final: 0.7090 (pp30) REVERT: A 179 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7983 (tpt90) REVERT: A 251 ASP cc_start: 0.8296 (m-30) cc_final: 0.7468 (t0) REVERT: A 308 ARG cc_start: 0.8352 (mmm160) cc_final: 0.7966 (mmm-85) REVERT: A 527 GLN cc_start: 0.8644 (mt0) cc_final: 0.8428 (pt0) REVERT: A 809 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: A 951 LEU cc_start: 0.8506 (mm) cc_final: 0.7943 (mm) REVERT: A 957 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: A 1001 ARG cc_start: 0.7478 (ttt90) cc_final: 0.7027 (ttm-80) REVERT: A 1132 MET cc_start: 0.7772 (mmt) cc_final: 0.7516 (tpp) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.3198 time to fit residues: 53.4450 Evaluate side-chains 125 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 957 TYR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.0070 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 90 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.154791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.125893 restraints weight = 14734.590| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 3.87 r_work: 0.3804 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.8313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7936 Z= 0.147 Angle : 0.765 13.209 10784 Z= 0.377 Chirality : 0.047 0.273 1200 Planarity : 0.005 0.063 1425 Dihedral : 5.077 21.626 1100 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.76 % Allowed : 18.87 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 990 helix: 0.69 (0.23), residues: 511 sheet: -0.68 (0.47), residues: 107 loop : -1.05 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 968 HIS 0.005 0.001 HIS A 174 PHE 0.027 0.002 PHE A 939 TYR 0.015 0.002 TYR A 248 ARG 0.013 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 445) hydrogen bonds : angle 5.33131 ( 1311) covalent geometry : bond 0.00319 ( 7936) covalent geometry : angle 0.76527 (10784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 HIS cc_start: 0.5756 (m90) cc_final: 0.5423 (m90) REVERT: A 104 GLN cc_start: 0.7488 (pp30) cc_final: 0.7028 (pp30) REVERT: A 179 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7940 (tpt90) REVERT: A 251 ASP cc_start: 0.8341 (m-30) cc_final: 0.7565 (t0) REVERT: A 308 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7914 (mmm-85) REVERT: A 848 PHE cc_start: 0.8388 (p90) cc_final: 0.8004 (p90) REVERT: A 951 LEU cc_start: 0.8609 (mm) cc_final: 0.8124 (mm) REVERT: A 957 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.5923 (m-80) REVERT: A 1001 ARG cc_start: 0.7287 (ttt90) cc_final: 0.6902 (ttm-80) REVERT: A 1132 MET cc_start: 0.7894 (mmt) cc_final: 0.7629 (tpp) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.3923 time to fit residues: 71.1704 Evaluate side-chains 122 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 957 TYR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 92 optimal weight: 0.0670 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.153701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.127818 restraints weight = 14376.265| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.57 r_work: 0.3811 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.8554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7936 Z= 0.161 Angle : 0.781 13.553 10784 Z= 0.384 Chirality : 0.047 0.241 1200 Planarity : 0.005 0.062 1425 Dihedral : 5.085 21.193 1100 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.64 % Allowed : 19.75 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.27), residues: 990 helix: 0.66 (0.23), residues: 511 sheet: -0.61 (0.48), residues: 107 loop : -1.17 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 968 HIS 0.015 0.001 HIS A 830 PHE 0.023 0.002 PHE A 939 TYR 0.022 0.002 TYR A 466 ARG 0.008 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 445) hydrogen bonds : angle 5.32266 ( 1311) covalent geometry : bond 0.00361 ( 7936) covalent geometry : angle 0.78127 (10784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4590.57 seconds wall clock time: 82 minutes 26.57 seconds (4946.57 seconds total)