Starting phenix.real_space_refine on Sat Aug 3 03:39:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5d_42982/08_2024/8v5d_42982.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5d_42982/08_2024/8v5d_42982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5d_42982/08_2024/8v5d_42982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5d_42982/08_2024/8v5d_42982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5d_42982/08_2024/8v5d_42982.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5d_42982/08_2024/8v5d_42982.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 43 5.16 5 C 4263 2.51 5 N 1173 2.21 5 O 1215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6694 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6694 Classifications: {'peptide': 851} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 793} Chain breaks: 6 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.53, per 1000 atoms: 0.68 Number of scatterers: 6694 At special positions: 0 Unit cell: (79.968, 94.129, 99.127, 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 43 16.00 O 1215 8.00 N 1173 7.00 C 4263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 46.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.731A pdb=" N LEU A 244 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.553A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.986A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.583A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 4.454A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 470 removed outlier: 3.653A pdb=" N ALA A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.510A pdb=" N LYS A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 removed outlier: 3.569A pdb=" N GLU A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 776 " --> pdb=" O PRO A 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 771 through 776' Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.582A pdb=" N LEU A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 804 " --> pdb=" O PHE A 800 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 3.527A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 4.245A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 915 through 923 Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 956 Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 989 removed outlier: 3.679A pdb=" N GLU A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 989 " --> pdb=" O MET A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1066 removed outlier: 3.783A pdb=" N PHE A1058 " --> pdb=" O GLU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.504A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1169 removed outlier: 3.670A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1211 Processing helix chain 'A' and resid 1219 through 1228 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.651A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS A 224 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 196 removed outlier: 6.196A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 438 Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA5, first strand: chain 'A' and resid 612 through 615 Processing sheet with id=AA6, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 7.664A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 831 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: 2.25 Time building geometry restraints manager: 2.75 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: 2216 1.34 - 1.46: 1501 1.46 - 1.58: 3083 1.58 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 6871 Sorted by residual: bond pdb=" CA VAL A 878 " pdb=" CB VAL A 878 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.21e+00 bond pdb=" N PRO A 246 " pdb=" CA PRO A 246 " ideal model delta sigma weight residual 1.469 1.482 -0.014 1.28e-02 6.10e+03 1.14e+00 bond pdb=" CA THR A 914 " pdb=" C THR A 914 " ideal model delta sigma weight residual 1.522 1.508 0.014 1.37e-02 5.33e+03 1.06e+00 bond pdb=" CA ALA A 604 " pdb=" C ALA A 604 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.28e-01 bond pdb=" N PRO A 163 " pdb=" CA PRO A 163 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 7.70e-01 ... (remaining 6866 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.56: 305 106.56 - 113.43: 3674 113.43 - 120.30: 2421 120.30 - 127.17: 2815 127.17 - 134.04: 124 Bond angle restraints: 9339 Sorted by residual: angle pdb=" CA GLY A1205 " pdb=" C GLY A1205 " pdb=" O GLY A1205 " ideal model delta sigma weight residual 122.37 120.22 2.15 7.30e-01 1.88e+00 8.67e+00 angle pdb=" CA GLY A1205 " pdb=" C GLY A1205 " pdb=" N MET A1206 " ideal model delta sigma weight residual 114.13 116.99 -2.86 1.11e+00 8.12e-01 6.62e+00 angle pdb=" O THR A 914 " pdb=" C THR A 914 " pdb=" N ALA A 915 " ideal model delta sigma weight residual 122.43 125.76 -3.33 1.46e+00 4.69e-01 5.20e+00 angle pdb=" CA THR A 914 " pdb=" C THR A 914 " pdb=" N ALA A 915 " ideal model delta sigma weight residual 118.41 115.43 2.98 1.34e+00 5.57e-01 4.93e+00 angle pdb=" C ILE A 245 " pdb=" N PRO A 246 " pdb=" CA PRO A 246 " ideal model delta sigma weight residual 119.84 122.59 -2.75 1.25e+00 6.40e-01 4.82e+00 ... (remaining 9334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 3875 16.24 - 32.48: 182 32.48 - 48.73: 35 48.73 - 64.97: 3 64.97 - 81.21: 2 Dihedral angle restraints: 4097 sinusoidal: 1648 harmonic: 2449 Sorted by residual: dihedral pdb=" CA SER A 810 " pdb=" C SER A 810 " pdb=" N GLN A 811 " pdb=" CA GLN A 811 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ARG A 869 " pdb=" CB ARG A 869 " pdb=" CG ARG A 869 " pdb=" CD ARG A 869 " ideal model delta sinusoidal sigma weight residual -180.00 -122.19 -57.81 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N PHE A1164 " pdb=" CA PHE A1164 " pdb=" CB PHE A1164 " pdb=" CG PHE A1164 " ideal model delta sinusoidal sigma weight residual -180.00 -128.38 -51.62 3 1.50e+01 4.44e-03 9.03e+00 ... (remaining 4094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 602 0.028 - 0.055: 258 0.055 - 0.083: 79 0.083 - 0.110: 53 0.110 - 0.138: 12 Chirality restraints: 1004 Sorted by residual: chirality pdb=" CA ILE A 245 " pdb=" N ILE A 245 " pdb=" C ILE A 245 " pdb=" CB ILE A 245 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL A 845 " pdb=" N VAL A 845 " pdb=" C VAL A 845 " pdb=" CB VAL A 845 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1001 not shown) Planarity restraints: 1214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 73 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 588 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 589 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 240 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.14e+00 pdb=" N PRO A 241 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.021 5.00e-02 4.00e+02 ... (remaining 1211 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 990 2.75 - 3.29: 6349 3.29 - 3.83: 11352 3.83 - 4.36: 12933 4.36 - 4.90: 22597 Nonbonded interactions: 54221 Sorted by model distance: nonbonded pdb=" O LYS A 990 " pdb=" OG SER A1055 " model vdw 2.219 3.040 nonbonded pdb=" O MET A 797 " pdb=" N VAL A 870 " model vdw 2.225 3.120 nonbonded pdb=" NH2 ARG A 417 " pdb=" O ILE A1079 " model vdw 2.227 3.120 nonbonded pdb=" O ASN A 795 " pdb=" OG SER A 799 " model vdw 2.245 3.040 nonbonded pdb=" O ALA A 957 " pdb=" OH TYR A 986 " model vdw 2.246 3.040 ... (remaining 54216 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 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: 1.600 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.650 Find NCS groups from input model: 0.070 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 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 0.035 6871 Z= 0.188 Angle : 0.519 5.071 9339 Z= 0.280 Chirality : 0.039 0.138 1004 Planarity : 0.004 0.050 1214 Dihedral : 9.897 81.209 2519 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.84 % Allowed : 4.26 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.80 (0.29), residues: 837 helix: 1.52 (0.28), residues: 345 sheet: 0.76 (0.61), residues: 82 loop : -0.33 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 859 HIS 0.005 0.001 HIS A 971 PHE 0.010 0.001 PHE A 389 TYR 0.010 0.001 TYR A1166 ARG 0.003 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 TYR cc_start: 0.6369 (t80) cc_final: 0.5555 (t80) REVERT: A 452 TYR cc_start: 0.7765 (t80) cc_final: 0.6909 (t80) REVERT: A 907 PHE cc_start: 0.6614 (t80) cc_final: 0.6252 (t80) REVERT: A 986 TYR cc_start: 0.7064 (m-80) cc_final: 0.6436 (m-80) outliers start: 13 outliers final: 4 residues processed: 178 average time/residue: 1.0454 time to fit residues: 196.7428 Evaluate side-chains 107 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 134 ASN A 161 GLN A 390 GLN A 398 GLN A 569 HIS A 805 HIS A 906 HIS ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 GLN A 968 GLN A 971 HIS A1157 ASN A1214 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6871 Z= 0.320 Angle : 0.731 9.872 9339 Z= 0.366 Chirality : 0.045 0.179 1004 Planarity : 0.005 0.056 1214 Dihedral : 4.613 35.880 928 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.26 % Allowed : 14.33 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.29), residues: 837 helix: 0.79 (0.27), residues: 347 sheet: 0.57 (0.57), residues: 83 loop : -0.46 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 918 HIS 0.007 0.002 HIS A 84 PHE 0.013 0.002 PHE A 197 TYR 0.031 0.002 TYR A 452 ARG 0.005 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 TYR cc_start: 0.6261 (t80) cc_final: 0.5439 (t80) REVERT: A 907 PHE cc_start: 0.6958 (t80) cc_final: 0.6581 (t80) REVERT: A 1153 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6207 (mp) outliers start: 30 outliers final: 10 residues processed: 125 average time/residue: 1.0745 time to fit residues: 142.6308 Evaluate side-chains 97 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.0070 chunk 76 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 144 GLN A 894 GLN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6871 Z= 0.215 Angle : 0.703 16.755 9339 Z= 0.340 Chirality : 0.043 0.252 1004 Planarity : 0.005 0.056 1214 Dihedral : 4.523 33.941 925 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.84 % Allowed : 17.59 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.29), residues: 837 helix: 0.83 (0.28), residues: 356 sheet: 0.37 (0.55), residues: 88 loop : -0.38 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 585 HIS 0.005 0.001 HIS A 84 PHE 0.008 0.001 PHE A 800 TYR 0.013 0.002 TYR A1166 ARG 0.010 0.001 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.665 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 375 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7195 (tp30) REVERT: A 398 GLN cc_start: 0.5646 (OUTLIER) cc_final: 0.5366 (pp30) REVERT: A 444 TYR cc_start: 0.6087 (t80) cc_final: 0.5509 (t80) REVERT: A 774 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.5489 (mpp) REVERT: A 907 PHE cc_start: 0.6816 (t80) cc_final: 0.6547 (t80) REVERT: A 1058 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: A 1062 GLU cc_start: 0.6048 (mm-30) cc_final: 0.4238 (pp20) REVERT: A 1153 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6084 (mp) REVERT: A 1163 MET cc_start: 0.6002 (tmm) cc_final: 0.5405 (tpt) outliers start: 20 outliers final: 5 residues processed: 112 average time/residue: 1.0211 time to fit residues: 121.3626 Evaluate side-chains 92 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1058 PHE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 398 GLN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6871 Z= 0.232 Angle : 0.721 13.873 9339 Z= 0.344 Chirality : 0.044 0.198 1004 Planarity : 0.005 0.053 1214 Dihedral : 4.593 31.843 925 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.26 % Allowed : 19.15 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.10 (0.29), residues: 837 helix: 0.59 (0.27), residues: 362 sheet: 0.15 (0.57), residues: 86 loop : -0.34 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 748 HIS 0.014 0.001 HIS A 971 PHE 0.024 0.002 PHE A 139 TYR 0.012 0.001 TYR A1166 ARG 0.010 0.001 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7253 (tp30) REVERT: A 907 PHE cc_start: 0.6856 (t80) cc_final: 0.6598 (t80) REVERT: A 1062 GLU cc_start: 0.6143 (mm-30) cc_final: 0.4255 (pp20) REVERT: A 1153 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6161 (mp) REVERT: A 1163 MET cc_start: 0.6059 (tmm) cc_final: 0.5422 (tpt) outliers start: 23 outliers final: 10 residues processed: 113 average time/residue: 0.9340 time to fit residues: 112.8908 Evaluate side-chains 95 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 6871 Z= 0.515 Angle : 0.938 13.167 9339 Z= 0.465 Chirality : 0.051 0.190 1004 Planarity : 0.006 0.072 1214 Dihedral : 5.491 31.691 925 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.57 % Favored : 93.31 % Rotamer: Outliers : 5.11 % Allowed : 19.72 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.91 (0.28), residues: 837 helix: -0.25 (0.27), residues: 356 sheet: -0.46 (0.59), residues: 76 loop : -0.86 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 801 HIS 0.012 0.002 HIS A 971 PHE 0.037 0.003 PHE A 139 TYR 0.023 0.003 TYR A 221 ARG 0.005 0.001 ARG A1142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.5716 (OUTLIER) cc_final: 0.5389 (ttm) REVERT: A 444 TYR cc_start: 0.6322 (t80) cc_final: 0.5160 (t80) REVERT: A 464 MET cc_start: 0.9201 (ptm) cc_final: 0.8777 (tmm) REVERT: A 877 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7065 (mpp) REVERT: A 907 PHE cc_start: 0.7022 (t80) cc_final: 0.6639 (t80) REVERT: A 986 TYR cc_start: 0.6720 (m-80) cc_final: 0.5004 (m-80) REVERT: A 1058 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.6153 (m-80) REVERT: A 1153 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6429 (mt) outliers start: 36 outliers final: 13 residues processed: 111 average time/residue: 0.9207 time to fit residues: 109.7484 Evaluate side-chains 91 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1058 PHE Chi-restraints excluded: chain A residue 1080 SER Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1206 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 82 optimal weight: 0.0170 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6871 Z= 0.212 Angle : 0.767 16.265 9339 Z= 0.362 Chirality : 0.046 0.159 1004 Planarity : 0.005 0.059 1214 Dihedral : 4.937 27.425 925 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.82 % Favored : 95.94 % Rotamer: Outliers : 2.41 % Allowed : 24.11 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.40 (0.29), residues: 837 helix: 0.24 (0.27), residues: 363 sheet: -0.64 (0.58), residues: 81 loop : -0.54 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 748 HIS 0.012 0.001 HIS A 971 PHE 0.023 0.002 PHE A 949 TYR 0.013 0.002 TYR A 831 ARG 0.007 0.001 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7286 (tp30) REVERT: A 444 TYR cc_start: 0.6068 (t80) cc_final: 0.5068 (t80) REVERT: A 461 LYS cc_start: 0.9090 (ptpt) cc_final: 0.8867 (mptp) REVERT: A 774 MET cc_start: 0.5247 (mpp) cc_final: 0.4708 (mpp) REVERT: A 795 ASN cc_start: 0.5839 (t0) cc_final: 0.5528 (t160) REVERT: A 877 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7045 (mpp) REVERT: A 907 PHE cc_start: 0.6841 (t80) cc_final: 0.6602 (t80) REVERT: A 986 TYR cc_start: 0.6567 (m-80) cc_final: 0.4844 (m-80) REVERT: A 1062 GLU cc_start: 0.5954 (mm-30) cc_final: 0.3764 (pt0) REVERT: A 1153 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6202 (mp) REVERT: A 1163 MET cc_start: 0.5980 (tmm) cc_final: 0.5455 (tpt) outliers start: 17 outliers final: 6 residues processed: 98 average time/residue: 0.9475 time to fit residues: 99.2829 Evaluate side-chains 88 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.0370 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6871 Z= 0.260 Angle : 0.785 18.124 9339 Z= 0.371 Chirality : 0.046 0.175 1004 Planarity : 0.006 0.065 1214 Dihedral : 4.886 28.253 925 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.85 % Favored : 93.91 % Rotamer: Outliers : 2.41 % Allowed : 24.68 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.45 (0.29), residues: 837 helix: 0.18 (0.27), residues: 363 sheet: -0.37 (0.60), residues: 78 loop : -0.62 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 748 HIS 0.012 0.001 HIS A 971 PHE 0.015 0.002 PHE A 139 TYR 0.012 0.001 TYR A1166 ARG 0.007 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7319 (tp30) REVERT: A 449 GLN cc_start: 0.6172 (OUTLIER) cc_final: 0.5950 (pp30) REVERT: A 774 MET cc_start: 0.5189 (mpp) cc_final: 0.4598 (mpp) REVERT: A 798 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7598 (pp) REVERT: A 877 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7350 (mpp) REVERT: A 907 PHE cc_start: 0.6921 (t80) cc_final: 0.6613 (t80) REVERT: A 986 TYR cc_start: 0.6644 (m-80) cc_final: 0.4835 (m-80) REVERT: A 1062 GLU cc_start: 0.5894 (mm-30) cc_final: 0.3694 (pt0) REVERT: A 1153 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6369 (mp) REVERT: A 1163 MET cc_start: 0.6127 (tmm) cc_final: 0.5565 (tpt) outliers start: 17 outliers final: 7 residues processed: 95 average time/residue: 0.9086 time to fit residues: 92.6680 Evaluate side-chains 88 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 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 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 ASN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6871 Z= 0.248 Angle : 0.789 17.431 9339 Z= 0.372 Chirality : 0.046 0.175 1004 Planarity : 0.005 0.059 1214 Dihedral : 4.844 27.128 925 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.02 % Favored : 94.74 % Rotamer: Outliers : 3.26 % Allowed : 24.11 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.36 (0.29), residues: 837 helix: 0.29 (0.27), residues: 363 sheet: -0.51 (0.59), residues: 81 loop : -0.58 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 748 HIS 0.012 0.001 HIS A 971 PHE 0.014 0.001 PHE A 949 TYR 0.012 0.001 TYR A1166 ARG 0.007 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7321 (tp30) REVERT: A 430 MET cc_start: 0.5724 (OUTLIER) cc_final: 0.5472 (ttm) REVERT: A 449 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5886 (pp30) REVERT: A 597 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7046 (mmt180) REVERT: A 774 MET cc_start: 0.5182 (mpp) cc_final: 0.4580 (mpp) REVERT: A 798 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7538 (pp) REVERT: A 877 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7288 (mpp) REVERT: A 907 PHE cc_start: 0.6903 (t80) cc_final: 0.6652 (t80) REVERT: A 1062 GLU cc_start: 0.5869 (mm-30) cc_final: 0.3717 (pt0) REVERT: A 1153 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6277 (mp) REVERT: A 1163 MET cc_start: 0.6104 (tmm) cc_final: 0.5555 (tpt) outliers start: 23 outliers final: 6 residues processed: 95 average time/residue: 0.9602 time to fit residues: 97.5121 Evaluate side-chains 89 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6871 Z= 0.231 Angle : 0.802 19.036 9339 Z= 0.373 Chirality : 0.046 0.175 1004 Planarity : 0.005 0.058 1214 Dihedral : 4.689 25.241 924 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.62 % Rotamer: Outliers : 2.13 % Allowed : 24.96 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.21 (0.30), residues: 837 helix: 0.47 (0.27), residues: 359 sheet: -0.52 (0.59), residues: 81 loop : -0.53 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 748 HIS 0.011 0.001 HIS A 971 PHE 0.015 0.001 PHE A 949 TYR 0.012 0.001 TYR A1166 ARG 0.009 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7323 (tp30) REVERT: A 449 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.5872 (pp30) REVERT: A 603 MET cc_start: 0.6946 (pmm) cc_final: 0.6696 (ppp) REVERT: A 774 MET cc_start: 0.5225 (mpp) cc_final: 0.4555 (mpp) REVERT: A 798 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7533 (pp) REVERT: A 877 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7257 (mpp) REVERT: A 907 PHE cc_start: 0.6895 (t80) cc_final: 0.6658 (t80) REVERT: A 1062 GLU cc_start: 0.5896 (mm-30) cc_final: 0.3822 (pt0) REVERT: A 1153 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6229 (mp) REVERT: A 1163 MET cc_start: 0.5997 (tmm) cc_final: 0.5433 (tpt) outliers start: 15 outliers final: 5 residues processed: 93 average time/residue: 0.9551 time to fit residues: 94.4043 Evaluate side-chains 87 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.0970 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.0270 chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 6871 Z= 0.228 Angle : 0.826 18.582 9339 Z= 0.381 Chirality : 0.046 0.196 1004 Planarity : 0.005 0.057 1214 Dihedral : 4.617 24.300 924 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 1.70 % Allowed : 25.82 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.16 (0.30), residues: 837 helix: 0.48 (0.27), residues: 361 sheet: -0.52 (0.59), residues: 81 loop : -0.46 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 748 HIS 0.011 0.001 HIS A 971 PHE 0.015 0.001 PHE A 949 TYR 0.011 0.001 TYR A1166 ARG 0.006 0.001 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6907 (mmt) cc_final: 0.6673 (ptt) REVERT: A 375 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7353 (tp30) REVERT: A 449 GLN cc_start: 0.6176 (OUTLIER) cc_final: 0.5807 (pp30) REVERT: A 603 MET cc_start: 0.6994 (pmm) cc_final: 0.6700 (ppp) REVERT: A 774 MET cc_start: 0.5298 (mpp) cc_final: 0.4601 (mpp) REVERT: A 798 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7537 (pp) REVERT: A 877 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7148 (mpp) REVERT: A 907 PHE cc_start: 0.6862 (t80) cc_final: 0.6640 (t80) REVERT: A 985 MET cc_start: 0.7661 (pp-130) cc_final: 0.7167 (ppp) REVERT: A 986 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.4703 (m-80) REVERT: A 1062 GLU cc_start: 0.5927 (mm-30) cc_final: 0.3886 (pt0) REVERT: A 1153 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6051 (mp) REVERT: A 1163 MET cc_start: 0.6096 (tmm) cc_final: 0.5536 (tpt) outliers start: 12 outliers final: 5 residues processed: 87 average time/residue: 1.1680 time to fit residues: 108.5218 Evaluate side-chains 83 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 986 TYR Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** 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 = 0.4985 r_free = 0.4985 target = 0.202984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.172508 restraints weight = 12041.023| |-----------------------------------------------------------------------------| r_work (start): 0.4658 rms_B_bonded: 3.96 r_work: 0.4509 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6871 Z= 0.233 Angle : 0.824 18.667 9339 Z= 0.386 Chirality : 0.047 0.222 1004 Planarity : 0.005 0.055 1214 Dihedral : 4.611 24.053 924 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 1.70 % Allowed : 26.24 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.30), residues: 837 helix: 0.49 (0.27), residues: 360 sheet: -0.48 (0.59), residues: 81 loop : -0.44 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 748 HIS 0.011 0.001 HIS A 971 PHE 0.014 0.001 PHE A 949 TYR 0.014 0.001 TYR A1139 ARG 0.009 0.001 ARG A 827 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2648.77 seconds wall clock time: 49 minutes 23.26 seconds (2963.26 seconds total)