Starting phenix.real_space_refine on Fri Mar 15 10:43:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3d_12704/03_2024/7o3d_12704.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3d_12704/03_2024/7o3d_12704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3d_12704/03_2024/7o3d_12704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3d_12704/03_2024/7o3d_12704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3d_12704/03_2024/7o3d_12704.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3d_12704/03_2024/7o3d_12704.pdb" } resolution = 3.71 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= -0.001 sd= 0.020 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 3650 2.51 5 N 983 2.21 5 O 1115 1.98 5 H 5694 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 11458 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 11458 Classifications: {'peptide': 709} Link IDs: {'PTRANS': 29, 'TRANS': 679} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.25, per 1000 atoms: 0.46 Number of scatterers: 11458 At special positions: 0 Unit cell: (65.412, 120.06, 101.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 1115 8.00 N 983 7.00 C 3650 6.00 H 5694 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1160 " distance=2.06 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: 8.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 3 sheets defined 59.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 340 through 360 removed outlier: 3.875A pdb=" N ASP A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.244A pdb=" N PHE A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.562A pdb=" N SER A 400 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 434 Processing helix chain 'A' and resid 618 through 622 removed outlier: 4.044A pdb=" N ASP A 622 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 637 through 650 removed outlier: 4.248A pdb=" N PHE A 641 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 734 removed outlier: 4.668A pdb=" N GLU A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 709 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 807 Processing helix chain 'A' and resid 818 through 835 removed outlier: 3.878A pdb=" N LYS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 removed outlier: 4.033A pdb=" N ASN A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 867 Processing helix chain 'A' and resid 871 through 886 Processing helix chain 'A' and resid 886 through 894 removed outlier: 3.545A pdb=" N LEU A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 902 Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 912 through 931 Processing helix chain 'A' and resid 934 through 939 Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 947 through 951 Processing helix chain 'A' and resid 955 through 970 removed outlier: 3.630A pdb=" N ILE A 960 " --> pdb=" O LYS A 956 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 986 through 994 Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1022 through 1024 No H-bonds generated for 'chain 'A' and resid 1022 through 1024' Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1040 through 1051 removed outlier: 3.765A pdb=" N ALA A1045 " --> pdb=" O PRO A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1063 removed outlier: 4.007A pdb=" N ILE A1057 " --> pdb=" O MET A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 Processing helix chain 'A' and resid 1074 through 1087 removed outlier: 3.573A pdb=" N TYR A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1103 removed outlier: 3.904A pdb=" N LEU A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP A1103 " --> pdb=" O LEU A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1126 Processing helix chain 'A' and resid 1169 through 1173 removed outlier: 3.943A pdb=" N LEU A1172 " --> pdb=" O GLY A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1226 through 1241 removed outlier: 3.579A pdb=" N ALA A1234 " --> pdb=" O GLU A1230 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A1236 " --> pdb=" O GLU A1232 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET A1241 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AA2, first strand: chain 'A' and resid 776 through 782 removed outlier: 3.659A pdb=" N ARG A 778 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 766 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 812 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 811 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1137 through 1141 removed outlier: 6.283A pdb=" N GLU A1201 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A1193 " --> pdb=" O THR A1199 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR A1199 " --> pdb=" O ILE A1193 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A1202 " --> pdb=" O VAL A1161 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 798 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: 4.13 Time building geometry restraints manager: 8.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5690 1.03 - 1.23: 103 1.23 - 1.43: 2362 1.43 - 1.63: 3388 1.63 - 1.83: 26 Bond restraints: 11569 Sorted by residual: bond pdb=" CB THR A 895 " pdb=" CG2 THR A 895 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" CD GLN A 707 " pdb=" OE1 GLN A 707 " ideal model delta sigma weight residual 1.231 1.206 0.025 1.90e-02 2.77e+03 1.69e+00 bond pdb=" NH1 ARG A 325 " pdb="HH12 ARG A 325 " ideal model delta sigma weight residual 0.860 0.835 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CA ILE A 705 " pdb=" C ILE A 705 " ideal model delta sigma weight residual 1.525 1.543 -0.018 1.59e-02 3.96e+03 1.34e+00 bond pdb=" NH1 ARG A1066 " pdb="HH12 ARG A1066 " ideal model delta sigma weight residual 0.860 0.837 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 11564 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.24: 384 107.24 - 113.92: 13641 113.92 - 120.61: 3942 120.61 - 127.30: 2904 127.30 - 133.98: 57 Bond angle restraints: 20928 Sorted by residual: angle pdb=" CA CYS A1152 " pdb=" CB CYS A1152 " pdb=" SG CYS A1152 " ideal model delta sigma weight residual 114.40 128.33 -13.93 2.30e+00 1.89e-01 3.67e+01 angle pdb=" CA ARG A1141 " pdb=" CB ARG A1141 " pdb=" CG ARG A1141 " ideal model delta sigma weight residual 114.10 122.25 -8.15 2.00e+00 2.50e-01 1.66e+01 angle pdb=" N CYS A1152 " pdb=" CA CYS A1152 " pdb=" CB CYS A1152 " ideal model delta sigma weight residual 111.20 106.07 5.13 1.62e+00 3.81e-01 1.00e+01 angle pdb=" N SER A 706 " pdb=" CA SER A 706 " pdb=" C SER A 706 " ideal model delta sigma weight residual 112.90 116.99 -4.09 1.31e+00 5.83e-01 9.75e+00 angle pdb=" N ILE A1179 " pdb=" CA ILE A1179 " pdb=" C ILE A1179 " ideal model delta sigma weight residual 109.34 115.82 -6.48 2.08e+00 2.31e-01 9.72e+00 ... (remaining 20923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 4951 16.42 - 32.85: 367 32.85 - 49.27: 83 49.27 - 65.70: 28 65.70 - 82.12: 10 Dihedral angle restraints: 5439 sinusoidal: 2968 harmonic: 2471 Sorted by residual: dihedral pdb=" CB CYS A1152 " pdb=" SG CYS A1152 " pdb=" SG CYS A1160 " pdb=" CB CYS A1160 " ideal model delta sinusoidal sigma weight residual -86.00 -12.83 -73.17 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CD ARG A1089 " pdb=" NE ARG A1089 " pdb=" CZ ARG A1089 " pdb=" NH1 ARG A1089 " ideal model delta sinusoidal sigma weight residual 0.00 33.56 -33.56 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" C CYS A1160 " pdb=" N CYS A1160 " pdb=" CA CYS A1160 " pdb=" CB CYS A1160 " ideal model delta harmonic sigma weight residual -122.60 -112.84 -9.76 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 5436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 705 0.051 - 0.102: 132 0.102 - 0.153: 34 0.153 - 0.205: 4 0.205 - 0.256: 3 Chirality restraints: 878 Sorted by residual: chirality pdb=" CA GLN A 707 " pdb=" N GLN A 707 " pdb=" C GLN A 707 " pdb=" CB GLN A 707 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA CYS A1160 " pdb=" N CYS A1160 " pdb=" C CYS A1160 " pdb=" CB CYS A1160 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LYS A1239 " pdb=" N LYS A1239 " pdb=" C LYS A1239 " pdb=" CB LYS A1239 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 875 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1109 " -0.432 9.50e-02 1.11e+02 1.55e-01 9.26e+01 pdb=" NE ARG A1109 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A1109 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A1109 " -0.076 2.00e-02 2.50e+03 pdb=" NH2 ARG A1109 " 0.062 2.00e-02 2.50e+03 pdb="HH11 ARG A1109 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A1109 " 0.094 2.00e-02 2.50e+03 pdb="HH21 ARG A1109 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A1109 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 325 " -0.028 9.50e-02 1.11e+02 5.50e-02 6.61e+01 pdb=" NE ARG A 325 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 325 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 325 " 0.100 2.00e-02 2.50e+03 pdb=" NH2 ARG A 325 " -0.042 2.00e-02 2.50e+03 pdb="HH11 ARG A 325 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 325 " -0.103 2.00e-02 2.50e+03 pdb="HH21 ARG A 325 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 325 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1066 " 0.138 9.50e-02 1.11e+02 6.85e-02 6.01e+01 pdb=" NE ARG A1066 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A1066 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG A1066 " -0.097 2.00e-02 2.50e+03 pdb=" NH2 ARG A1066 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A1066 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A1066 " 0.096 2.00e-02 2.50e+03 pdb="HH21 ARG A1066 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1066 " 0.001 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 325 2.12 - 2.74: 20927 2.74 - 3.36: 32125 3.36 - 3.98: 38275 3.98 - 4.60: 60392 Nonbonded interactions: 152044 Sorted by model distance: nonbonded pdb=" OE2 GLU A 866 " pdb="HH22 ARG A 882 " model vdw 1.503 1.850 nonbonded pdb=" HZ1 LYS A 728 " pdb=" O ILE A 904 " model vdw 1.589 1.850 nonbonded pdb="HH11 ARG A 826 " pdb=" OE2 GLU A 829 " model vdw 1.610 1.850 nonbonded pdb=" OE1 GLU A 914 " pdb=" H GLU A 914 " model vdw 1.612 1.850 nonbonded pdb=" OE1 GLU A 934 " pdb=" HH TYR A 998 " model vdw 1.636 1.850 ... (remaining 152039 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.170 Extract box with map and model: 4.100 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 38.450 Find NCS groups from input model: 0.200 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 0.043 5875 Z= 0.196 Angle : 0.768 13.934 7943 Z= 0.451 Chirality : 0.046 0.256 878 Planarity : 0.014 0.221 1038 Dihedral : 13.165 82.121 2230 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.31), residues: 697 helix: 0.11 (0.26), residues: 336 sheet: -1.32 (0.62), residues: 62 loop : -0.65 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.007 TRP A1225 HIS 0.021 0.004 HIS A1027 PHE 0.023 0.003 PHE A 424 TYR 0.036 0.006 TYR A 392 ARG 0.050 0.006 ARG A1109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 ARG cc_start: 0.7584 (mpt180) cc_final: 0.6980 (mmp80) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3389 time to fit residues: 39.4983 Evaluate side-chains 68 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5875 Z= 0.244 Angle : 0.581 6.453 7943 Z= 0.321 Chirality : 0.040 0.153 878 Planarity : 0.004 0.040 1038 Dihedral : 4.148 14.934 768 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.94 % Allowed : 8.95 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.32), residues: 697 helix: 0.60 (0.26), residues: 349 sheet: -1.54 (0.59), residues: 64 loop : -0.71 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1146 HIS 0.006 0.001 HIS A1167 PHE 0.015 0.002 PHE A1133 TYR 0.014 0.002 TYR A 876 ARG 0.003 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 1.124 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 629 ARG cc_start: 0.7527 (mpt180) cc_final: 0.6746 (mmp80) REVERT: A 634 PHE cc_start: 0.6753 (m-80) cc_final: 0.6365 (m-80) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 0.3276 time to fit residues: 34.2463 Evaluate side-chains 72 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1241 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5875 Z= 0.157 Angle : 0.502 6.422 7943 Z= 0.271 Chirality : 0.039 0.143 878 Planarity : 0.004 0.028 1038 Dihedral : 4.044 15.467 768 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.94 % Allowed : 8.95 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.32), residues: 697 helix: 1.00 (0.27), residues: 349 sheet: -1.61 (0.58), residues: 64 loop : -0.62 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1225 HIS 0.004 0.001 HIS A1167 PHE 0.013 0.001 PHE A1133 TYR 0.012 0.001 TYR A 876 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.957 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 629 ARG cc_start: 0.7514 (mpt180) cc_final: 0.6747 (mmp80) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.3444 time to fit residues: 35.7678 Evaluate side-chains 72 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1241 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5875 Z= 0.190 Angle : 0.504 6.426 7943 Z= 0.274 Chirality : 0.039 0.140 878 Planarity : 0.004 0.033 1038 Dihedral : 4.139 16.212 768 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.10 % Allowed : 10.05 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.32), residues: 697 helix: 0.99 (0.27), residues: 352 sheet: -1.64 (0.59), residues: 63 loop : -0.75 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1146 HIS 0.005 0.001 HIS A1167 PHE 0.015 0.001 PHE A1056 TYR 0.014 0.001 TYR A 876 ARG 0.002 0.000 ARG A1166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 ARG cc_start: 0.7547 (mpt180) cc_final: 0.6733 (mmp80) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.3266 time to fit residues: 34.2621 Evaluate side-chains 72 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1241 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5875 Z= 0.179 Angle : 0.488 6.387 7943 Z= 0.265 Chirality : 0.038 0.143 878 Planarity : 0.003 0.036 1038 Dihedral : 4.154 16.440 768 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.94 % Allowed : 11.62 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.32), residues: 697 helix: 1.05 (0.27), residues: 352 sheet: -1.75 (0.58), residues: 63 loop : -0.75 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1146 HIS 0.005 0.001 HIS A1167 PHE 0.012 0.001 PHE A 641 TYR 0.014 0.001 TYR A 336 ARG 0.001 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.904 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 629 ARG cc_start: 0.7504 (mpt180) cc_final: 0.6651 (mmp80) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 0.3159 time to fit residues: 32.5182 Evaluate side-chains 74 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1241 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5875 Z= 0.152 Angle : 0.474 6.382 7943 Z= 0.254 Chirality : 0.038 0.142 878 Planarity : 0.003 0.035 1038 Dihedral : 4.088 15.007 768 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.26 % Allowed : 11.93 % Favored : 86.81 % 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: 0.20 (0.32), residues: 697 helix: 1.19 (0.27), residues: 352 sheet: -1.77 (0.58), residues: 63 loop : -0.67 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1146 HIS 0.005 0.001 HIS A1167 PHE 0.011 0.001 PHE A 641 TYR 0.011 0.001 TYR A 876 ARG 0.001 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.950 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: A 629 ARG cc_start: 0.7495 (mpt180) cc_final: 0.6635 (mmp80) outliers start: 8 outliers final: 7 residues processed: 75 average time/residue: 0.3121 time to fit residues: 32.6122 Evaluate side-chains 75 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 707 GLN Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1241 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5875 Z= 0.169 Angle : 0.478 6.369 7943 Z= 0.258 Chirality : 0.038 0.141 878 Planarity : 0.003 0.036 1038 Dihedral : 4.094 14.875 768 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.41 % Allowed : 12.24 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.32), residues: 697 helix: 1.18 (0.27), residues: 353 sheet: -1.80 (0.59), residues: 63 loop : -0.69 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 918 HIS 0.005 0.001 HIS A1167 PHE 0.014 0.001 PHE A 641 TYR 0.012 0.001 TYR A 876 ARG 0.001 0.000 ARG A1109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.906 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: A 629 ARG cc_start: 0.7530 (mpt180) cc_final: 0.6610 (mmp80) outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 0.3301 time to fit residues: 34.8536 Evaluate side-chains 75 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 707 GLN Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1241 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5875 Z= 0.181 Angle : 0.488 6.403 7943 Z= 0.264 Chirality : 0.038 0.143 878 Planarity : 0.004 0.037 1038 Dihedral : 4.127 15.097 768 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.26 % Allowed : 13.19 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.32), residues: 697 helix: 1.18 (0.27), residues: 352 sheet: -1.80 (0.59), residues: 63 loop : -0.73 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 918 HIS 0.005 0.001 HIS A1167 PHE 0.011 0.001 PHE A 641 TYR 0.013 0.001 TYR A 876 ARG 0.002 0.000 ARG A1109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.922 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: A 629 ARG cc_start: 0.7519 (mpt180) cc_final: 0.6656 (mmp80) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.3170 time to fit residues: 34.0463 Evaluate side-chains 76 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 707 GLN Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1241 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5875 Z= 0.238 Angle : 0.522 6.392 7943 Z= 0.287 Chirality : 0.039 0.145 878 Planarity : 0.004 0.037 1038 Dihedral : 4.286 15.124 768 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.57 % Allowed : 13.19 % Favored : 85.24 % 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: -0.09 (0.32), residues: 697 helix: 0.98 (0.27), residues: 352 sheet: -1.82 (0.61), residues: 63 loop : -0.91 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 918 HIS 0.005 0.001 HIS A1167 PHE 0.009 0.001 PHE A 380 TYR 0.016 0.001 TYR A 876 ARG 0.002 0.000 ARG A1166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.969 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: A 411 GLU cc_start: 0.7825 (mp0) cc_final: 0.7568 (mp0) REVERT: A 629 ARG cc_start: 0.7596 (mpt180) cc_final: 0.7097 (mpt180) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.3204 time to fit residues: 33.9548 Evaluate side-chains 77 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 707 GLN Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1241 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5875 Z= 0.137 Angle : 0.481 6.342 7943 Z= 0.256 Chirality : 0.038 0.144 878 Planarity : 0.003 0.036 1038 Dihedral : 4.106 15.412 768 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.41 % Allowed : 13.34 % Favored : 85.24 % 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: 0.31 (0.33), residues: 697 helix: 1.26 (0.27), residues: 352 sheet: -1.76 (0.61), residues: 63 loop : -0.60 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1146 HIS 0.003 0.001 HIS A1167 PHE 0.009 0.001 PHE A 634 TYR 0.010 0.001 TYR A 876 ARG 0.001 0.000 ARG A 882 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.921 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: A 411 GLU cc_start: 0.7821 (mp0) cc_final: 0.7272 (mp0) REVERT: A 629 ARG cc_start: 0.7556 (mpt180) cc_final: 0.6611 (mmp80) REVERT: A 801 ASN cc_start: 0.8249 (m110) cc_final: 0.7959 (m110) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.3081 time to fit residues: 34.0407 Evaluate side-chains 80 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 707 GLN Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1160 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.118947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104450 restraints weight = 56995.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107915 restraints weight = 24648.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.110069 restraints weight = 13675.590| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5875 Z= 0.161 Angle : 0.482 6.385 7943 Z= 0.259 Chirality : 0.038 0.140 878 Planarity : 0.003 0.037 1038 Dihedral : 4.081 15.129 768 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.10 % Allowed : 13.97 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.33), residues: 697 helix: 1.28 (0.27), residues: 352 sheet: -1.72 (0.62), residues: 63 loop : -0.65 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1146 HIS 0.004 0.001 HIS A1167 PHE 0.032 0.001 PHE A 634 TYR 0.012 0.001 TYR A 876 ARG 0.002 0.000 ARG A1109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2741.98 seconds wall clock time: 48 minutes 54.41 seconds (2934.41 seconds total)