Starting phenix.real_space_refine on Wed Sep 17 03:43:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh4_50439/09_2025/9fh4_50439.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh4_50439/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fh4_50439/09_2025/9fh4_50439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh4_50439/09_2025/9fh4_50439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fh4_50439/09_2025/9fh4_50439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh4_50439/09_2025/9fh4_50439.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.00, per 1000 atoms: 0.29 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: 0.31 Conformation dependent library (CDL) restraints added in 89.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.11 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: 0.76 Time building geometry restraints manager: 0.45 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: 1.390 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: 0.020 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.074 0.023 TYR I 10 HIS 0.009 0.004 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.01159 ( 1645) covalent geometry : angle 1.84383 ( 2200) hydrogen bonds : bond 0.15945 ( 18) hydrogen bonds : angle 9.38733 ( 54) *********************** 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 : 0.104 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: 0.7540 (ttm) REVERT: C 35 MET cc_start: 0.8208 (tmm) cc_final: 0.7863 (ttm) REVERT: D 35 MET cc_start: 0.8172 (tpp) cc_final: 0.7706 (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: 0.7543 (ttm) REVERT: I 35 MET cc_start: 0.7580 (tmm) cc_final: 0.7218 (ttm) REVERT: J 35 MET cc_start: 0.7174 (tpp) cc_final: 0.4246 (ppp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0647 time to fit residues: 4.6475 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 : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.129028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.114555 restraints weight = 9964.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.118918 restraints weight = 2967.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.121664 restraints weight = 1358.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.123146 restraints weight = 794.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.124275 restraints weight = 570.709| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1645 Z= 0.189 Angle : 0.536 4.087 2200 Z= 0.308 Chirality : 0.064 0.151 280 Planarity : 0.002 0.006 265 Dihedral : 5.553 14.576 235 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.42 % Allowed : 4.24 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.47), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 10 HIS 0.003 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 1645) covalent geometry : angle 0.53643 ( 2200) hydrogen bonds : bond 0.02850 ( 18) hydrogen bonds : angle 5.50846 ( 54) *********************** 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: 4 poor density : 36 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.0580 time to fit residues: 3.1214 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 : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain J residue 27 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.4144 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.126370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.111796 restraints weight = 10175.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.116309 restraints weight = 3018.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.118995 restraints weight = 1368.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.120402 restraints weight = 797.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.121445 restraints weight = 576.998| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4321 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= 0.131 Angle : 0.479 3.519 2200 Z= 0.267 Chirality : 0.062 0.150 280 Planarity : 0.001 0.005 265 Dihedral : 4.629 13.550 235 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.82 % Allowed : 7.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.48), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.72 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR E 10 HIS 0.001 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 1645) covalent geometry : angle 0.47929 ( 2200) hydrogen bonds : bond 0.01459 ( 18) hydrogen bonds : angle 4.39014 ( 54) *********************** 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 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.0524 time to fit residues: 2.6224 Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.129694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.115131 restraints weight = 9702.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.119743 restraints weight = 2904.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.122468 restraints weight = 1275.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.124111 restraints weight = 736.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.125085 restraints weight = 502.928| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4641 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= 0.081 Angle : 0.483 4.142 2200 Z= 0.247 Chirality : 0.063 0.147 280 Planarity : 0.001 0.006 265 Dihedral : 4.232 12.401 235 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.50), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.52 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 10 HIS 0.001 0.000 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00168 ( 1645) covalent geometry : angle 0.48258 ( 2200) hydrogen bonds : bond 0.01531 ( 18) hydrogen bonds : angle 4.22034 ( 54) *********************** 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 34 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.0536 time to fit residues: 2.4950 Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.127145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.112883 restraints weight = 9979.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.117251 restraints weight = 2955.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.119917 restraints weight = 1313.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.121382 restraints weight = 766.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.122345 restraints weight = 550.499| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4881 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= 0.118 Angle : 0.473 4.073 2200 Z= 0.250 Chirality : 0.061 0.140 280 Planarity : 0.001 0.004 265 Dihedral : 4.095 13.406 235 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.61 % Allowed : 8.48 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.50), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.49 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 10 HIS 0.001 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 1645) covalent geometry : angle 0.47287 ( 2200) hydrogen bonds : bond 0.01327 ( 18) hydrogen bonds : angle 4.00016 ( 54) *********************** 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 35 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.0523 time to fit residues: 2.4709 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 : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 0.0970 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.0010 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.132892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.118218 restraints weight = 9519.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.122993 restraints weight = 2954.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.125956 restraints weight = 1337.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.127718 restraints weight = 746.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.128669 restraints weight = 488.668| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 1645 Z= 0.066 Angle : 0.485 4.660 2200 Z= 0.235 Chirality : 0.062 0.141 280 Planarity : 0.001 0.003 265 Dihedral : 3.740 12.106 235 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.52), 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 TYR 0.003 0.001 TYR A 10 HIS 0.001 0.000 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00146 ( 1645) covalent geometry : angle 0.48546 ( 2200) hydrogen bonds : bond 0.01332 ( 18) hydrogen bonds : angle 3.87745 ( 54) *********************** 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 34 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 MET cc_start: 0.8983 (ttm) cc_final: 0.8691 (ttm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0563 time to fit residues: 2.5849 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 : 0.097 ------------------------------------------------------------------------------- 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: 6.9990 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.123217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.108844 restraints weight = 10491.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.112957 restraints weight = 3074.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.115474 restraints weight = 1413.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.116931 restraints weight = 849.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.117919 restraints weight = 619.059| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1645 Z= 0.153 Angle : 0.527 4.237 2200 Z= 0.269 Chirality : 0.061 0.142 280 Planarity : 0.001 0.005 265 Dihedral : 3.992 12.469 235 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.61 % Allowed : 12.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.52), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 10 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 1645) covalent geometry : angle 0.52693 ( 2200) hydrogen bonds : bond 0.01320 ( 18) hydrogen bonds : angle 3.63152 ( 54) *********************** 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 32 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 MET cc_start: 0.9011 (ttm) cc_final: 0.8671 (ttm) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0547 time to fit residues: 2.3926 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 : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.0170 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9820 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.127374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.112941 restraints weight = 10120.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.117236 restraints weight = 2951.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.119896 restraints weight = 1323.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.121446 restraints weight = 784.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.122450 restraints weight = 550.724| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 1645 Z= 0.069 Angle : 0.469 4.335 2200 Z= 0.231 Chirality : 0.061 0.137 280 Planarity : 0.001 0.003 265 Dihedral : 3.718 12.285 235 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.52), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.28 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 10 HIS 0.002 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00141 ( 1645) covalent geometry : angle 0.46910 ( 2200) hydrogen bonds : bond 0.01177 ( 18) hydrogen bonds : angle 3.60969 ( 54) *********************** 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 38 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 MET cc_start: 0.8941 (ttm) cc_final: 0.8711 (ttm) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0589 time to fit residues: 3.0018 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.129732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.115262 restraints weight = 9810.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.119663 restraints weight = 2909.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.122378 restraints weight = 1311.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.123973 restraints weight = 769.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.124918 restraints weight = 532.693| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 1645 Z= 0.070 Angle : 0.470 4.647 2200 Z= 0.232 Chirality : 0.062 0.137 280 Planarity : 0.001 0.004 265 Dihedral : 3.634 15.567 235 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.53), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.22 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR A 10 HIS 0.001 0.000 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00146 ( 1645) covalent geometry : angle 0.47010 ( 2200) hydrogen bonds : bond 0.01122 ( 18) hydrogen bonds : angle 3.61529 ( 54) *********************** 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 35 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 MET cc_start: 0.9007 (ttm) cc_final: 0.8745 (ttm) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0597 time to fit residues: 2.8091 Evaluate side-chains 35 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.092 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.126726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.112565 restraints weight = 10146.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.116775 restraints weight = 3014.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.119358 restraints weight = 1384.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.120920 restraints weight = 822.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.121799 restraints weight = 571.372| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5704 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= 0.088 Angle : 0.477 4.774 2200 Z= 0.237 Chirality : 0.061 0.139 280 Planarity : 0.001 0.004 265 Dihedral : 3.648 15.940 235 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.54), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.17 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 10 HIS 0.001 0.000 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 1645) covalent geometry : angle 0.47736 ( 2200) hydrogen bonds : bond 0.01221 ( 18) hydrogen bonds : angle 3.59693 ( 54) ********************** 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 35 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 MET cc_start: 0.9019 (ttm) cc_final: 0.8775 (ttm) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.0590 time to fit residues: 2.7032 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 : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.125373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.111261 restraints weight = 10277.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.115415 restraints weight = 3048.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.117992 restraints weight = 1393.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.119564 restraints weight = 825.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.120578 restraints weight = 580.299| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1645 Z= 0.087 Angle : 0.482 4.248 2200 Z= 0.238 Chirality : 0.061 0.138 280 Planarity : 0.001 0.004 265 Dihedral : 3.632 15.355 235 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 12.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.54), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.18 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR A 10 HIS 0.001 0.000 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00170 ( 1645) covalent geometry : angle 0.48209 ( 2200) hydrogen bonds : bond 0.01195 ( 18) hydrogen bonds : angle 3.49724 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1240.22 seconds wall clock time: 21 minutes 52.77 seconds (1312.77 seconds total)