Starting phenix.real_space_refine on Thu Jul 24 10:15:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ey0_31374/07_2025/7ey0_31374.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ey0_31374/07_2025/7ey0_31374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ey0_31374/07_2025/7ey0_31374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ey0_31374/07_2025/7ey0_31374.map" model { file = "/net/cci-nas-00/data/ceres_data/7ey0_31374/07_2025/7ey0_31374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ey0_31374/07_2025/7ey0_31374.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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 24 5.16 5 C 3824 2.51 5 N 994 2.21 5 O 1121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5963 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 905 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 903 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "B" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 564 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 7, 'TRANS': 65} Chain breaks: 4 Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1359 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 7 Time building chain proxies: 4.12, per 1000 atoms: 0.69 Number of scatterers: 5963 At special positions: 0 Unit cell: (79.92, 117.72, 123.12, 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 24 16.00 O 1121 8.00 N 994 7.00 C 3824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 86 " distance=2.07 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 791.0 milliseconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 17 sheets defined 8.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.623A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.526A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.561A pdb=" N THR H 90 " --> pdb=" O VAL H 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.511A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 364 through 370 removed outlier: 4.452A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 390 removed outlier: 3.584A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.473A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 4 through 7 current: chain 'A' and resid 78 through 83 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 50 removed outlier: 6.678A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 35 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 97 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 93 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 104 through 108 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.526A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N THR L 69 " --> pdb=" O THR L 25 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 36 through 38 Processing sheet with id=AA8, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'L' and resid 91 through 92 removed outlier: 3.874A pdb=" N LEU L 96 " --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358 removed outlier: 4.256A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.595A pdb=" N SER B 61 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.577A pdb=" N VAL B 88 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 97 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 90 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 50 through 55 removed outlier: 3.774A pdb=" N ASP N 53 " --> pdb=" O ARG N 273 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 63 through 64 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 63 through 64 current: chain 'N' and resid 116 through 121 removed outlier: 3.767A pdb=" N ASN N 164 " --> pdb=" O GLU N 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 163 through 164 current: chain 'N' and resid 200 through 205 removed outlier: 5.953A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 255 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: 1.60 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 949 1.31 - 1.45: 2124 1.45 - 1.59: 3010 1.59 - 1.74: 0 1.74 - 1.88: 31 Bond restraints: 6114 Sorted by residual: bond pdb=" C PRO B 96 " pdb=" O PRO B 96 " ideal model delta sigma weight residual 1.233 1.172 0.060 1.16e-02 7.43e+03 2.71e+01 bond pdb=" C PRO B 6 " pdb=" O PRO B 6 " ideal model delta sigma weight residual 1.246 1.204 0.041 8.50e-03 1.38e+04 2.37e+01 bond pdb=" C PRO B 42 " pdb=" O PRO B 42 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" N PRO B 96 " pdb=" CA PRO B 96 " ideal model delta sigma weight residual 1.467 1.420 0.047 1.21e-02 6.83e+03 1.53e+01 bond pdb=" CA PRO B 96 " pdb=" CB PRO B 96 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.34e-02 5.57e+03 9.76e+00 ... (remaining 6109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 8131 3.09 - 6.19: 144 6.19 - 9.28: 10 9.28 - 12.37: 5 12.37 - 15.46: 3 Bond angle restraints: 8293 Sorted by residual: angle pdb=" C PRO B 96 " pdb=" CA PRO B 96 " pdb=" CB PRO B 96 " ideal model delta sigma weight residual 111.46 100.25 11.21 1.29e+00 6.01e-01 7.55e+01 angle pdb=" C PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta sigma weight residual 110.29 97.27 13.02 1.64e+00 3.72e-01 6.30e+01 angle pdb=" C GLN B 87 " pdb=" CA GLN B 87 " pdb=" CB GLN B 87 " ideal model delta sigma weight residual 111.74 99.57 12.17 1.59e+00 3.96e-01 5.86e+01 angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 129.86 -15.46 2.30e+00 1.89e-01 4.52e+01 angle pdb=" C GLN B 95 " pdb=" CA GLN B 95 " pdb=" CB GLN B 95 " ideal model delta sigma weight residual 109.45 99.97 9.48 1.45e+00 4.76e-01 4.27e+01 ... (remaining 8288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3172 17.35 - 34.70: 290 34.70 - 52.05: 59 52.05 - 69.41: 15 69.41 - 86.76: 10 Dihedral angle restraints: 3546 sinusoidal: 1375 harmonic: 2171 Sorted by residual: dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual -86.00 -13.29 -72.71 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" C PHE B 98 " pdb=" N PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta harmonic sigma weight residual -122.60 -102.26 -20.34 0 2.50e+00 1.60e-01 6.62e+01 dihedral pdb=" CA THR H 101 " pdb=" C THR H 101 " pdb=" N TYR H 102 " pdb=" CA TYR H 102 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.54e+01 ... (remaining 3543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 788 0.092 - 0.183: 84 0.183 - 0.275: 14 0.275 - 0.367: 4 0.367 - 0.458: 2 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA PHE B 98 " pdb=" N PHE B 98 " pdb=" C PHE B 98 " pdb=" CB PHE B 98 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA GLN B 5 " pdb=" N GLN B 5 " pdb=" C GLN B 5 " pdb=" CB GLN B 5 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA GLN B 95 " pdb=" N GLN B 95 " pdb=" C GLN B 95 " pdb=" CB GLN B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 889 not shown) Planarity restraints: 1058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO L 80 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 97 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL B 97 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL B 97 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE B 98 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 33 " -0.015 2.00e-02 2.50e+03 2.09e-02 8.71e+00 pdb=" CG TYR H 33 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR H 33 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR H 33 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 33 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR H 33 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 33 " 0.003 2.00e-02 2.50e+03 ... (remaining 1055 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 185 2.66 - 3.22: 5667 3.22 - 3.78: 8987 3.78 - 4.34: 12996 4.34 - 4.90: 21645 Nonbonded interactions: 49480 Sorted by model distance: nonbonded pdb=" OE2 GLU H 6 " pdb=" N GLY H 111 " model vdw 2.105 3.120 nonbonded pdb=" OH TYR N 37 " pdb=" O LEU N 54 " model vdw 2.149 3.040 nonbonded pdb=" OG SER R 469 " pdb=" OE1 GLU R 471 " model vdw 2.170 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.196 3.040 nonbonded pdb=" NE2 GLN B 5 " pdb=" SG CYS B 21 " model vdw 2.199 3.480 ... (remaining 49475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.530 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.007 0.068 6122 Z= 0.391 Angle : 1.026 15.464 8309 Z= 0.621 Chirality : 0.064 0.458 892 Planarity : 0.007 0.097 1058 Dihedral : 14.511 86.758 2138 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.24 % Favored : 87.34 % Rotamer: Outliers : 3.08 % Allowed : 0.62 % Favored : 96.31 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.31), residues: 719 helix: -2.18 (1.14), residues: 21 sheet: -1.17 (0.36), residues: 217 loop : -1.88 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 47 HIS 0.012 0.002 HIS B 32 PHE 0.030 0.002 PHE B 98 TYR 0.048 0.002 TYR H 33 ARG 0.018 0.001 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.25239 ( 111) hydrogen bonds : angle 11.12190 ( 255) SS BOND : bond 0.01457 ( 8) SS BOND : angle 4.62628 ( 16) covalent geometry : bond 0.00717 ( 6114) covalent geometry : angle 1.00684 ( 8293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 471 GLU cc_start: 0.7604 (mp0) cc_final: 0.7357 (mp0) REVERT: B 38 PRO cc_start: 0.8488 (OUTLIER) cc_final: 0.8284 (Cg_endo) REVERT: B 40 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7686 (mm110) REVERT: B 47 TYR cc_start: 0.4554 (OUTLIER) cc_final: 0.4258 (p90) REVERT: B 87 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: B 88 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8696 (t) REVERT: B 95 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: N 43 PHE cc_start: 0.5948 (p90) cc_final: 0.5165 (p90) REVERT: N 84 LEU cc_start: 0.7640 (mt) cc_final: 0.7405 (mp) REVERT: N 111 ASP cc_start: 0.8045 (t70) cc_final: 0.7562 (p0) REVERT: N 129 LYS cc_start: 0.7819 (mtmt) cc_final: 0.7553 (ttpp) REVERT: N 132 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7793 (mt-10) REVERT: N 133 PHE cc_start: 0.7780 (m-80) cc_final: 0.7492 (m-10) REVERT: N 171 VAL cc_start: 0.8677 (t) cc_final: 0.8441 (p) REVERT: N 202 LYS cc_start: 0.8234 (mttt) cc_final: 0.7936 (mttp) REVERT: N 231 ILE cc_start: 0.8945 (mm) cc_final: 0.8556 (pt) REVERT: N 237 ARG cc_start: 0.8228 (ptm160) cc_final: 0.7905 (ptp90) outliers start: 20 outliers final: 3 residues processed: 206 average time/residue: 0.2246 time to fit residues: 57.2578 Evaluate side-chains 173 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 PRO Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 42 PRO Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 95 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124938 restraints weight = 9546.980| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.21 r_work: 0.3421 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6122 Z= 0.164 Angle : 0.685 10.720 8309 Z= 0.359 Chirality : 0.046 0.171 892 Planarity : 0.005 0.069 1058 Dihedral : 8.689 89.937 845 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.92 % Allowed : 10.62 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.32), residues: 719 helix: -2.00 (1.18), residues: 21 sheet: -0.86 (0.37), residues: 213 loop : -1.62 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 64 HIS 0.006 0.002 HIS B 32 PHE 0.016 0.001 PHE R 456 TYR 0.021 0.001 TYR H 33 ARG 0.006 0.001 ARG N 273 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 111) hydrogen bonds : angle 8.08234 ( 255) SS BOND : bond 0.00550 ( 8) SS BOND : angle 3.53076 ( 16) covalent geometry : bond 0.00383 ( 6114) covalent geometry : angle 0.66782 ( 8293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 5 GLN cc_start: 0.6857 (tp40) cc_final: 0.6373 (tp40) REVERT: B 47 TYR cc_start: 0.5322 (OUTLIER) cc_final: 0.4845 (p90) REVERT: B 95 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: N 43 PHE cc_start: 0.6723 (p90) cc_final: 0.5407 (p90) REVERT: N 62 VAL cc_start: 0.8620 (t) cc_final: 0.8083 (p) REVERT: N 111 ASP cc_start: 0.8409 (t70) cc_final: 0.7741 (p0) REVERT: N 190 ARG cc_start: 0.7190 (mtp-110) cc_final: 0.6647 (mpt180) outliers start: 19 outliers final: 11 residues processed: 197 average time/residue: 0.2476 time to fit residues: 62.2392 Evaluate side-chains 179 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 0.0000 chunk 67 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.153250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126778 restraints weight = 9601.754| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.36 r_work: 0.3422 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6122 Z= 0.132 Angle : 0.625 9.382 8309 Z= 0.330 Chirality : 0.045 0.157 892 Planarity : 0.004 0.062 1058 Dihedral : 6.246 61.588 827 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.85 % Allowed : 13.85 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.31), residues: 719 helix: -2.31 (1.03), residues: 21 sheet: -0.65 (0.37), residues: 218 loop : -1.47 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 64 HIS 0.004 0.001 HIS L 34 PHE 0.029 0.002 PHE N 32 TYR 0.014 0.001 TYR N 170 ARG 0.003 0.001 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 111) hydrogen bonds : angle 7.35944 ( 255) SS BOND : bond 0.00508 ( 8) SS BOND : angle 3.25858 ( 16) covalent geometry : bond 0.00306 ( 6114) covalent geometry : angle 0.60889 ( 8293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8233 (tm-30) REVERT: L 82 ASP cc_start: 0.8557 (m-30) cc_final: 0.8261 (m-30) REVERT: R 434 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8197 (pt) REVERT: R 442 ASP cc_start: 0.8271 (m-30) cc_final: 0.8014 (m-30) REVERT: R 472 ILE cc_start: 0.9483 (mm) cc_final: 0.9257 (mt) REVERT: B 47 TYR cc_start: 0.5018 (OUTLIER) cc_final: 0.4715 (p90) REVERT: B 94 ASP cc_start: 0.8228 (t0) cc_final: 0.7749 (t70) REVERT: B 95 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: B 103 LYS cc_start: 0.8341 (tptm) cc_final: 0.8094 (tptm) REVERT: N 43 PHE cc_start: 0.6892 (p90) cc_final: 0.5595 (p90) REVERT: N 111 ASP cc_start: 0.8477 (t70) cc_final: 0.7753 (p0) REVERT: N 112 SER cc_start: 0.8795 (p) cc_final: 0.8149 (t) REVERT: N 190 ARG cc_start: 0.7254 (mtp-110) cc_final: 0.6736 (mpt180) outliers start: 25 outliers final: 15 residues processed: 187 average time/residue: 0.2794 time to fit residues: 67.7878 Evaluate side-chains 179 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 354 ASN B 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118989 restraints weight = 9707.131| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.85 r_work: 0.3392 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6122 Z= 0.210 Angle : 0.669 9.946 8309 Z= 0.351 Chirality : 0.046 0.162 892 Planarity : 0.005 0.058 1058 Dihedral : 5.885 50.350 827 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 5.69 % Allowed : 14.77 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.31), residues: 719 helix: -2.54 (0.97), residues: 21 sheet: -0.81 (0.35), residues: 228 loop : -1.50 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 64 HIS 0.006 0.001 HIS N 49 PHE 0.027 0.002 PHE H 67 TYR 0.015 0.002 TYR L 49 ARG 0.004 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 111) hydrogen bonds : angle 6.89365 ( 255) SS BOND : bond 0.00469 ( 8) SS BOND : angle 3.40223 ( 16) covalent geometry : bond 0.00483 ( 6114) covalent geometry : angle 0.65236 ( 8293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8282 (tm-30) REVERT: L 82 ASP cc_start: 0.8559 (m-30) cc_final: 0.8242 (m-30) REVERT: R 434 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8156 (pt) REVERT: R 442 ASP cc_start: 0.8274 (m-30) cc_final: 0.7961 (m-30) REVERT: R 472 ILE cc_start: 0.9463 (mm) cc_final: 0.9228 (mt) REVERT: B 46 MET cc_start: 0.5694 (ttp) cc_final: 0.5377 (ttt) REVERT: B 47 TYR cc_start: 0.4825 (OUTLIER) cc_final: 0.4299 (p90) REVERT: B 94 ASP cc_start: 0.8073 (t0) cc_final: 0.7645 (t70) REVERT: N 43 PHE cc_start: 0.6779 (p90) cc_final: 0.5481 (p90) REVERT: N 115 GLN cc_start: 0.8727 (mm110) cc_final: 0.8473 (mm-40) REVERT: N 190 ARG cc_start: 0.7290 (mtp-110) cc_final: 0.7036 (mpt180) outliers start: 37 outliers final: 26 residues processed: 181 average time/residue: 0.2154 time to fit residues: 49.3766 Evaluate side-chains 181 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 2 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN B 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118093 restraints weight = 9600.920| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.88 r_work: 0.3403 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6122 Z= 0.151 Angle : 0.622 9.043 8309 Z= 0.326 Chirality : 0.045 0.146 892 Planarity : 0.004 0.052 1058 Dihedral : 5.544 49.236 824 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.23 % Allowed : 17.23 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.32), residues: 719 helix: -2.57 (0.98), residues: 21 sheet: -0.70 (0.35), residues: 230 loop : -1.41 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 64 HIS 0.004 0.001 HIS L 34 PHE 0.046 0.001 PHE H 67 TYR 0.014 0.001 TYR L 49 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 111) hydrogen bonds : angle 6.67553 ( 255) SS BOND : bond 0.00396 ( 8) SS BOND : angle 3.07580 ( 16) covalent geometry : bond 0.00353 ( 6114) covalent geometry : angle 0.60755 ( 8293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 26 GLU cc_start: 0.8025 (tp30) cc_final: 0.7754 (tp30) REVERT: R 442 ASP cc_start: 0.8297 (m-30) cc_final: 0.8010 (m-30) REVERT: R 472 ILE cc_start: 0.9465 (mm) cc_final: 0.9207 (mt) REVERT: B 46 MET cc_start: 0.5744 (ttp) cc_final: 0.5519 (ttp) REVERT: B 47 TYR cc_start: 0.5001 (OUTLIER) cc_final: 0.4306 (p90) REVERT: B 72 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7305 (mp) REVERT: N 43 PHE cc_start: 0.6695 (p90) cc_final: 0.5354 (p90) REVERT: N 115 GLN cc_start: 0.8586 (mm110) cc_final: 0.8328 (mm-40) REVERT: N 190 ARG cc_start: 0.7214 (mtp-110) cc_final: 0.6952 (mmp-170) outliers start: 34 outliers final: 25 residues processed: 183 average time/residue: 0.2128 time to fit residues: 50.4380 Evaluate side-chains 183 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 0.0670 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.150072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118755 restraints weight = 9487.038| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.78 r_work: 0.3405 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6122 Z= 0.150 Angle : 0.616 8.901 8309 Z= 0.325 Chirality : 0.044 0.153 892 Planarity : 0.004 0.053 1058 Dihedral : 5.461 47.920 824 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.31 % Allowed : 18.77 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.31), residues: 719 helix: -2.52 (1.00), residues: 21 sheet: -0.54 (0.36), residues: 224 loop : -1.42 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 64 HIS 0.004 0.001 HIS L 34 PHE 0.042 0.002 PHE H 67 TYR 0.014 0.001 TYR L 49 ARG 0.004 0.000 ARG R 357 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 111) hydrogen bonds : angle 6.55194 ( 255) SS BOND : bond 0.00364 ( 8) SS BOND : angle 3.01753 ( 16) covalent geometry : bond 0.00354 ( 6114) covalent geometry : angle 0.60256 ( 8293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: H 26 GLU cc_start: 0.8013 (tp30) cc_final: 0.7751 (tp30) REVERT: R 442 ASP cc_start: 0.8301 (m-30) cc_final: 0.8012 (m-30) REVERT: R 465 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: R 471 GLU cc_start: 0.8275 (pm20) cc_final: 0.7751 (mp0) REVERT: B 46 MET cc_start: 0.5789 (ttp) cc_final: 0.5549 (ttp) REVERT: B 47 TYR cc_start: 0.4970 (OUTLIER) cc_final: 0.4270 (p90) REVERT: B 72 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7281 (mp) REVERT: N 43 PHE cc_start: 0.6775 (p90) cc_final: 0.5387 (p90) REVERT: N 115 GLN cc_start: 0.8602 (mm110) cc_final: 0.8346 (mm-40) REVERT: N 190 ARG cc_start: 0.7266 (mtp-110) cc_final: 0.6996 (mmp-170) REVERT: N 240 THR cc_start: 0.8492 (m) cc_final: 0.8288 (m) outliers start: 28 outliers final: 23 residues processed: 180 average time/residue: 0.1975 time to fit residues: 45.2757 Evaluate side-chains 180 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 81 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117941 restraints weight = 9623.706| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.85 r_work: 0.3398 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6122 Z= 0.187 Angle : 0.652 9.672 8309 Z= 0.345 Chirality : 0.045 0.174 892 Planarity : 0.004 0.049 1058 Dihedral : 5.547 46.767 824 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.23 % Allowed : 19.54 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.32), residues: 719 helix: -2.69 (0.94), residues: 21 sheet: -0.56 (0.36), residues: 224 loop : -1.37 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 33 HIS 0.003 0.001 HIS L 34 PHE 0.020 0.001 PHE N 168 TYR 0.014 0.001 TYR L 49 ARG 0.003 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 111) hydrogen bonds : angle 6.47179 ( 255) SS BOND : bond 0.00501 ( 8) SS BOND : angle 3.13892 ( 16) covalent geometry : bond 0.00436 ( 6114) covalent geometry : angle 0.63807 ( 8293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 26 GLU cc_start: 0.8021 (tp30) cc_final: 0.7522 (tp30) REVERT: R 442 ASP cc_start: 0.8320 (m-30) cc_final: 0.8045 (m-30) REVERT: R 465 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8247 (tm-30) REVERT: B 47 TYR cc_start: 0.5003 (OUTLIER) cc_final: 0.4572 (p90) REVERT: B 72 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7305 (mp) REVERT: N 61 ASN cc_start: 0.3918 (m-40) cc_final: 0.3712 (m-40) REVERT: N 115 GLN cc_start: 0.8678 (mm110) cc_final: 0.8419 (mm-40) REVERT: N 190 ARG cc_start: 0.7385 (mtp-110) cc_final: 0.7022 (mmp-170) outliers start: 34 outliers final: 24 residues processed: 181 average time/residue: 0.2069 time to fit residues: 47.3167 Evaluate side-chains 181 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.0060 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.149044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117558 restraints weight = 9516.866| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.03 r_work: 0.3393 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6122 Z= 0.166 Angle : 0.658 12.210 8309 Z= 0.347 Chirality : 0.045 0.164 892 Planarity : 0.004 0.048 1058 Dihedral : 5.455 45.672 824 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.46 % Allowed : 21.08 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.32), residues: 719 helix: -2.58 (0.97), residues: 21 sheet: -0.55 (0.36), residues: 229 loop : -1.31 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 33 HIS 0.004 0.001 HIS L 34 PHE 0.013 0.001 PHE H 67 TYR 0.018 0.001 TYR N 170 ARG 0.004 0.000 ARG R 357 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 111) hydrogen bonds : angle 6.37600 ( 255) SS BOND : bond 0.00489 ( 8) SS BOND : angle 3.05857 ( 16) covalent geometry : bond 0.00390 ( 6114) covalent geometry : angle 0.64517 ( 8293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: H 26 GLU cc_start: 0.8129 (tp30) cc_final: 0.7639 (tp30) REVERT: L 38 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7906 (tm-30) REVERT: R 442 ASP cc_start: 0.8279 (m-30) cc_final: 0.7975 (m-30) REVERT: B 46 MET cc_start: 0.6183 (ttp) cc_final: 0.5821 (ttt) REVERT: B 47 TYR cc_start: 0.4810 (OUTLIER) cc_final: 0.4302 (p90) REVERT: B 72 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7263 (mp) REVERT: N 61 ASN cc_start: 0.5991 (m-40) cc_final: 0.4118 (p0) REVERT: N 115 GLN cc_start: 0.8638 (mm110) cc_final: 0.8374 (mm-40) REVERT: N 190 ARG cc_start: 0.7444 (mtp-110) cc_final: 0.7039 (mmp-170) REVERT: N 224 GLU cc_start: 0.7512 (tp30) cc_final: 0.6737 (mm-30) outliers start: 29 outliers final: 24 residues processed: 178 average time/residue: 0.2137 time to fit residues: 47.8115 Evaluate side-chains 183 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 50 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.150771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124276 restraints weight = 9639.466| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.24 r_work: 0.3375 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6122 Z= 0.154 Angle : 0.655 12.182 8309 Z= 0.344 Chirality : 0.045 0.185 892 Planarity : 0.004 0.048 1058 Dihedral : 5.388 45.643 824 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.46 % Allowed : 21.08 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.32), residues: 719 helix: -2.38 (1.04), residues: 21 sheet: -0.53 (0.36), residues: 231 loop : -1.34 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.004 0.001 HIS L 34 PHE 0.022 0.001 PHE N 168 TYR 0.014 0.001 TYR L 49 ARG 0.005 0.000 ARG N 273 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 111) hydrogen bonds : angle 6.29814 ( 255) SS BOND : bond 0.00439 ( 8) SS BOND : angle 3.02096 ( 16) covalent geometry : bond 0.00362 ( 6114) covalent geometry : angle 0.64232 ( 8293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: H 26 GLU cc_start: 0.8041 (tp30) cc_final: 0.7539 (tp30) REVERT: R 442 ASP cc_start: 0.8259 (m-30) cc_final: 0.7981 (m-30) REVERT: B 39 ARG cc_start: 0.7843 (tpm170) cc_final: 0.7538 (mmp80) REVERT: B 47 TYR cc_start: 0.4834 (OUTLIER) cc_final: 0.4399 (p90) REVERT: B 72 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7278 (mp) REVERT: N 61 ASN cc_start: 0.6974 (m-40) cc_final: 0.6512 (m-40) REVERT: N 115 GLN cc_start: 0.8595 (mm110) cc_final: 0.8381 (mm-40) REVERT: N 190 ARG cc_start: 0.7465 (mtp-110) cc_final: 0.7099 (mmp-170) REVERT: N 224 GLU cc_start: 0.7362 (tp30) cc_final: 0.6564 (mm-30) outliers start: 29 outliers final: 25 residues processed: 178 average time/residue: 0.2112 time to fit residues: 47.1357 Evaluate side-chains 185 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 280 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 48 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.150856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124788 restraints weight = 9606.438| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.04 r_work: 0.3389 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6122 Z= 0.148 Angle : 0.658 12.029 8309 Z= 0.346 Chirality : 0.044 0.157 892 Planarity : 0.004 0.048 1058 Dihedral : 5.364 48.696 824 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.15 % Allowed : 21.85 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.32), residues: 719 helix: -2.14 (1.16), residues: 21 sheet: -0.55 (0.36), residues: 234 loop : -1.32 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 35 HIS 0.004 0.001 HIS L 34 PHE 0.013 0.001 PHE H 67 TYR 0.014 0.001 TYR N 170 ARG 0.006 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 111) hydrogen bonds : angle 6.18754 ( 255) SS BOND : bond 0.00438 ( 8) SS BOND : angle 2.89153 ( 16) covalent geometry : bond 0.00350 ( 6114) covalent geometry : angle 0.64656 ( 8293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: H 26 GLU cc_start: 0.7987 (tp30) cc_final: 0.7491 (tp30) REVERT: L 38 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8338 (tp-100) REVERT: R 442 ASP cc_start: 0.8261 (m-30) cc_final: 0.8030 (m-30) REVERT: B 39 ARG cc_start: 0.7764 (tpm170) cc_final: 0.7558 (mmp80) REVERT: B 47 TYR cc_start: 0.4785 (OUTLIER) cc_final: 0.3992 (p90) REVERT: B 72 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7279 (mp) REVERT: N 115 GLN cc_start: 0.8532 (mm110) cc_final: 0.8304 (mm-40) REVERT: N 168 PHE cc_start: 0.8596 (t80) cc_final: 0.8303 (t80) REVERT: N 190 ARG cc_start: 0.7443 (mtp-110) cc_final: 0.7087 (mmp-170) REVERT: N 224 GLU cc_start: 0.7281 (tp30) cc_final: 0.6520 (mm-30) outliers start: 27 outliers final: 23 residues processed: 175 average time/residue: 0.2574 time to fit residues: 56.7476 Evaluate side-chains 181 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 280 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 50 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 0.0000 chunk 46 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.152038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124898 restraints weight = 9731.159| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.50 r_work: 0.3385 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6122 Z= 0.129 Angle : 0.652 11.770 8309 Z= 0.343 Chirality : 0.044 0.201 892 Planarity : 0.004 0.048 1058 Dihedral : 5.282 51.166 824 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.00 % Allowed : 21.69 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.32), residues: 719 helix: -2.13 (1.14), residues: 21 sheet: -0.39 (0.36), residues: 234 loop : -1.27 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.006 0.001 HIS L 34 PHE 0.013 0.001 PHE R 456 TYR 0.013 0.001 TYR L 49 ARG 0.006 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02766 ( 111) hydrogen bonds : angle 6.10780 ( 255) SS BOND : bond 0.00376 ( 8) SS BOND : angle 2.76439 ( 16) covalent geometry : bond 0.00305 ( 6114) covalent geometry : angle 0.64140 ( 8293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4552.70 seconds wall clock time: 80 minutes 54.93 seconds (4854.93 seconds total)