Starting phenix.real_space_refine on Wed Jul 23 13:25:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh4_50439/07_2025/9fh4_50439.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh4_50439/07_2025/9fh4_50439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fh4_50439/07_2025/9fh4_50439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh4_50439/07_2025/9fh4_50439.map" model { file = "/net/cci-nas-00/data/ceres_data/9fh4_50439/07_2025/9fh4_50439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh4_50439/07_2025/9fh4_50439.cif" } resolution = 4.0 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= 0.318 sd= 1.537 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 1060 2.51 5 N 290 2.21 5 O 280 1.98 5 H 1800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3440 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 278 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "D" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 278 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "E" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "F" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 278 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "H" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 278 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "J" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 278 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Time building chain proxies: 2.18, per 1000 atoms: 0.63 Number of scatterers: 3440 At special positions: 0 Unit cell: (64.464, 62.016, 45.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 280 8.00 N 290 7.00 C 1060 6.00 H 1800 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 210.3 milliseconds 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.543A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N HIS C 13 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 12 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR C 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N HIS E 13 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N HIS G 13 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL E 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR G 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N HIS I 13 " --> pdb=" O TYR G 10 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL G 12 " --> pdb=" O HIS I 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 removed outlier: 6.661A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.445A pdb=" N ALA A 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 30 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA E 30 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA G 30 " --> pdb=" O ILE I 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.776A pdb=" N MET A 35 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET C 35 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET E 35 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET G 35 " --> pdb=" O VAL I 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.863A pdb=" N ILE B 31 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE D 32 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY B 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 31 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE F 32 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY D 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE F 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE H 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY F 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE H 31 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE J 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY H 33 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.533A pdb=" N VAL D 40 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL F 40 " --> pdb=" O ILE H 41 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL H 40 " --> pdb=" O ILE J 41 " (cutoff:3.500A) 18 hydrogen bonds defined for protein. 54 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: 1.30 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 1800 1.13 - 1.30: 265 1.30 - 1.47: 521 1.47 - 1.64: 839 1.64 - 1.81: 20 Bond restraints: 3445 Sorted by residual: bond pdb=" CD2 TYR A 10 " pdb=" HD2 TYR A 10 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL A 18 " pdb=" H VAL A 18 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD1 TYR I 10 " pdb=" HD1 TYR I 10 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY I 33 " pdb=" H GLY I 33 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL A 40 " pdb=" H VAL A 40 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 3440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 4679 1.88 - 3.76: 1088 3.76 - 5.63: 360 5.63 - 7.51: 149 7.51 - 9.39: 4 Bond angle restraints: 6280 Sorted by residual: angle pdb=" N HIS G 13 " pdb=" CA HIS G 13 " pdb=" C HIS G 13 " ideal model delta sigma weight residual 109.07 118.46 -9.39 1.52e+00 4.33e-01 3.82e+01 angle pdb=" N HIS E 13 " pdb=" CA HIS E 13 " pdb=" C HIS E 13 " ideal model delta sigma weight residual 109.07 118.31 -9.24 1.52e+00 4.33e-01 3.70e+01 angle pdb=" N HIS C 13 " pdb=" CA HIS C 13 " pdb=" C HIS C 13 " ideal model delta sigma weight residual 109.07 118.04 -8.97 1.52e+00 4.33e-01 3.48e+01 angle pdb=" N HIS I 13 " pdb=" CA HIS I 13 " pdb=" C HIS I 13 " ideal model delta sigma weight residual 109.07 116.53 -7.46 1.52e+00 4.33e-01 2.41e+01 angle pdb=" CB HIS A 13 " pdb=" CG HIS A 13 " pdb=" CD2 HIS A 13 " ideal model delta sigma weight residual 131.20 125.34 5.86 1.30e+00 5.92e-01 2.03e+01 ... (remaining 6275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.82: 1308 12.82 - 25.63: 59 25.63 - 38.45: 71 38.45 - 51.27: 28 51.27 - 64.08: 74 Dihedral angle restraints: 1540 sinusoidal: 885 harmonic: 655 Sorted by residual: dihedral pdb=" CA GLY H 25 " pdb=" C GLY H 25 " pdb=" N SER H 26 " pdb=" CA SER H 26 " ideal model delta harmonic sigma weight residual -180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLY F 25 " pdb=" C GLY F 25 " pdb=" N SER F 26 " pdb=" CA SER F 26 " ideal model delta harmonic sigma weight residual -180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLY J 25 " pdb=" C GLY J 25 " pdb=" N SER J 26 " pdb=" CA SER J 26 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 1537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 129 0.065 - 0.129: 100 0.129 - 0.193: 40 0.193 - 0.258: 8 0.258 - 0.322: 3 Chirality restraints: 280 Sorted by residual: chirality pdb=" CA LYS I 28 " pdb=" N LYS I 28 " pdb=" C LYS I 28 " pdb=" CB LYS I 28 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA HIS E 13 " pdb=" N HIS E 13 " pdb=" C HIS E 13 " pdb=" CB HIS E 13 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA HIS G 13 " pdb=" N HIS G 13 " pdb=" C HIS G 13 " pdb=" CB HIS G 13 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 277 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 10 " 0.077 2.00e-02 2.50e+03 4.04e-02 4.90e+01 pdb=" CG TYR I 10 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR I 10 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR I 10 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR I 10 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR I 10 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR I 10 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR I 10 " 0.088 2.00e-02 2.50e+03 pdb=" HD1 TYR I 10 " -0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR I 10 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR I 10 " -0.020 2.00e-02 2.50e+03 pdb=" HE2 TYR I 10 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 27 " -0.060 2.00e-02 2.50e+03 5.41e-02 4.39e+01 pdb=" CG ASN B 27 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 27 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 27 " 0.057 2.00e-02 2.50e+03 pdb="HD21 ASN B 27 " 0.028 2.00e-02 2.50e+03 pdb="HD22 ASN B 27 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 10 " 0.050 2.00e-02 2.50e+03 3.12e-02 2.91e+01 pdb=" CG TYR G 10 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR G 10 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR G 10 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR G 10 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR G 10 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR G 10 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR G 10 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 TYR G 10 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR G 10 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR G 10 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR G 10 " -0.031 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 417 2.29 - 2.86: 7246 2.86 - 3.44: 8676 3.44 - 4.02: 12310 4.02 - 4.60: 17125 Nonbonded interactions: 45774 Sorted by model distance: nonbonded pdb=" O SER B 26 " pdb=" HG SER D 26 " model vdw 1.706 2.450 nonbonded pdb=" O SER D 26 " pdb=" HG SER F 26 " model vdw 1.709 2.450 nonbonded pdb=" HG SER E 26 " pdb=" O SER G 26 " model vdw 1.722 2.450 nonbonded pdb=" O GLY A 37 " pdb=" HH TYR E 10 " model vdw 1.726 2.450 nonbonded pdb=" HG SER G 26 " pdb=" O SER I 26 " model vdw 1.728 2.450 ... (remaining 45769 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.570 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.012 0.034 1645 Z= 0.741 Angle : 1.844 9.391 2200 Z= 1.193 Chirality : 0.097 0.322 280 Planarity : 0.009 0.042 265 Dihedral : 11.016 37.634 560 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.45), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.57 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS C 14 TYR 0.074 0.023 TYR I 10 Details of bonding type rmsd hydrogen bonds : bond 0.15945 ( 18) hydrogen bonds : angle 9.38733 ( 54) covalent geometry : bond 0.01159 ( 1645) covalent geometry : angle 1.84383 ( 2200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8265 (tmm) cc_final: 0.7546 (ttm) REVERT: C 35 MET cc_start: 0.8208 (tmm) cc_final: 0.7862 (ttm) REVERT: D 35 MET cc_start: 0.8172 (tpp) cc_final: 0.7737 (ttm) REVERT: E 35 MET cc_start: 0.8091 (tmm) cc_final: 0.7807 (ttm) REVERT: G 35 MET cc_start: 0.7838 (tmm) cc_final: 0.7541 (ttm) REVERT: I 35 MET cc_start: 0.7580 (tmm) cc_final: 0.7213 (ttm) REVERT: J 35 MET cc_start: 0.7174 (tpp) cc_final: 0.4230 (ppp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1528 time to fit residues: 10.9944 Evaluate side-chains 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.134551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.118725 restraints weight = 9371.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.123544 restraints weight = 2976.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.126442 restraints weight = 1349.880| |-----------------------------------------------------------------------------| r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1645 Z= 0.126 Angle : 0.513 4.421 2200 Z= 0.289 Chirality : 0.064 0.146 280 Planarity : 0.002 0.006 265 Dihedral : 5.296 14.547 235 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.21 % Allowed : 6.06 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.47), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 13 TYR 0.006 0.001 TYR G 10 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 18) hydrogen bonds : angle 5.54656 ( 54) covalent geometry : bond 0.00248 ( 1645) covalent geometry : angle 0.51345 ( 2200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 35 MET cc_start: 0.8436 (tpp) cc_final: 0.5040 (ppp) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1222 time to fit residues: 6.4303 Evaluate side-chains 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 41 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.130003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.114112 restraints weight = 9578.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.118892 restraints weight = 3012.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.121778 restraints weight = 1390.923| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1645 Z= 0.120 Angle : 0.482 3.606 2200 Z= 0.262 Chirality : 0.062 0.146 280 Planarity : 0.001 0.005 265 Dihedral : 4.544 13.590 235 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.21 % Allowed : 8.48 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.49), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 13 TYR 0.004 0.001 TYR G 10 Details of bonding type rmsd hydrogen bonds : bond 0.01615 ( 18) hydrogen bonds : angle 4.47198 ( 54) covalent geometry : bond 0.00242 ( 1645) covalent geometry : angle 0.48220 ( 2200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8007 (m-80) cc_final: 0.7683 (m-80) outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 0.1740 time to fit residues: 8.2174 Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 0.4980 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.131990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.115581 restraints weight = 9645.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.120458 restraints weight = 3001.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.123347 restraints weight = 1380.667| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1645 Z= 0.108 Angle : 0.486 4.477 2200 Z= 0.251 Chirality : 0.062 0.142 280 Planarity : 0.001 0.004 265 Dihedral : 4.191 13.159 235 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.61 % Allowed : 10.30 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.50), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 13 TYR 0.004 0.001 TYR G 10 Details of bonding type rmsd hydrogen bonds : bond 0.01161 ( 18) hydrogen bonds : angle 4.05553 ( 54) covalent geometry : bond 0.00214 ( 1645) covalent geometry : angle 0.48578 ( 2200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8030 (m-80) cc_final: 0.7730 (m-80) outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1387 time to fit residues: 6.6216 Evaluate side-chains 32 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.130082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.114939 restraints weight = 9849.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.119457 restraints weight = 2996.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.122240 restraints weight = 1364.943| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1645 Z= 0.089 Angle : 0.475 4.655 2200 Z= 0.241 Chirality : 0.062 0.142 280 Planarity : 0.001 0.003 265 Dihedral : 3.913 12.669 235 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.50), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.49 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 13 TYR 0.004 0.001 TYR G 10 Details of bonding type rmsd hydrogen bonds : bond 0.01320 ( 18) hydrogen bonds : angle 3.85387 ( 54) covalent geometry : bond 0.00177 ( 1645) covalent geometry : angle 0.47474 ( 2200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8032 (m-80) cc_final: 0.7745 (m-80) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2638 time to fit residues: 11.9904 Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.125131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.110098 restraints weight = 10321.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.114390 restraints weight = 3099.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.116942 restraints weight = 1418.173| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1645 Z= 0.144 Angle : 0.510 4.203 2200 Z= 0.265 Chirality : 0.061 0.141 280 Planarity : 0.001 0.005 265 Dihedral : 4.041 14.122 235 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.51), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.39 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 14 TYR 0.004 0.001 TYR G 10 Details of bonding type rmsd hydrogen bonds : bond 0.01327 ( 18) hydrogen bonds : angle 3.70087 ( 54) covalent geometry : bond 0.00283 ( 1645) covalent geometry : angle 0.50980 ( 2200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 MET cc_start: 0.9074 (ttm) cc_final: 0.8811 (ttm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1433 time to fit residues: 5.8493 Evaluate side-chains 31 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.127545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.112695 restraints weight = 10074.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.116988 restraints weight = 3045.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.119533 restraints weight = 1384.851| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1645 Z= 0.087 Angle : 0.471 4.179 2200 Z= 0.239 Chirality : 0.062 0.141 280 Planarity : 0.001 0.003 265 Dihedral : 3.792 12.990 235 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.61 % Allowed : 11.52 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.51), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 14 TYR 0.003 0.001 TYR G 10 Details of bonding type rmsd hydrogen bonds : bond 0.01197 ( 18) hydrogen bonds : angle 3.56600 ( 54) covalent geometry : bond 0.00175 ( 1645) covalent geometry : angle 0.47132 ( 2200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 MET cc_start: 0.9065 (ttm) cc_final: 0.8718 (ttm) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.1426 time to fit residues: 6.4322 Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.128944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.114273 restraints weight = 9876.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.118613 restraints weight = 2953.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.121272 restraints weight = 1333.439| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1645 Z= 0.082 Angle : 0.471 4.389 2200 Z= 0.237 Chirality : 0.061 0.139 280 Planarity : 0.001 0.003 265 Dihedral : 3.721 14.287 235 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.61 % Allowed : 10.30 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.51), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 14 TYR 0.004 0.001 TYR G 10 Details of bonding type rmsd hydrogen bonds : bond 0.01122 ( 18) hydrogen bonds : angle 3.60413 ( 54) covalent geometry : bond 0.00167 ( 1645) covalent geometry : angle 0.47058 ( 2200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1376 time to fit residues: 6.6130 Evaluate side-chains 32 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.124970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.110523 restraints weight = 10076.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.114712 restraints weight = 3010.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.117317 restraints weight = 1375.403| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1645 Z= 0.125 Angle : 0.490 4.365 2200 Z= 0.255 Chirality : 0.061 0.141 280 Planarity : 0.001 0.005 265 Dihedral : 3.900 14.748 235 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.52), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 14 TYR 0.004 0.001 TYR I 10 Details of bonding type rmsd hydrogen bonds : bond 0.01184 ( 18) hydrogen bonds : angle 3.53305 ( 54) covalent geometry : bond 0.00248 ( 1645) covalent geometry : angle 0.48958 ( 2200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1519 time to fit residues: 6.6529 Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.127923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.113410 restraints weight = 9838.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.117629 restraints weight = 2880.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.120252 restraints weight = 1316.445| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1645 Z= 0.079 Angle : 0.488 4.906 2200 Z= 0.240 Chirality : 0.062 0.139 280 Planarity : 0.001 0.003 265 Dihedral : 3.764 15.725 235 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.52), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 14 TYR 0.004 0.000 TYR G 10 Details of bonding type rmsd hydrogen bonds : bond 0.01120 ( 18) hydrogen bonds : angle 3.58871 ( 54) covalent geometry : bond 0.00167 ( 1645) covalent geometry : angle 0.48774 ( 2200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2366 time to fit residues: 12.1454 Evaluate side-chains 34 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.131025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.114798 restraints weight = 9719.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.119432 restraints weight = 2978.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.122316 restraints weight = 1388.071| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1645 Z= 0.082 Angle : 0.482 4.492 2200 Z= 0.241 Chirality : 0.062 0.138 280 Planarity : 0.001 0.004 265 Dihedral : 3.681 15.250 235 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.52), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 13 TYR 0.003 0.000 TYR G 10 Details of bonding type rmsd hydrogen bonds : bond 0.01150 ( 18) hydrogen bonds : angle 3.52938 ( 54) covalent geometry : bond 0.00166 ( 1645) covalent geometry : angle 0.48153 ( 2200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3193.09 seconds wall clock time: 59 minutes 4.34 seconds (3544.34 seconds total)