Starting phenix.real_space_refine on Fri Feb 14 02:16:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqr_16799/02_2025/8cqr_16799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqr_16799/02_2025/8cqr_16799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cqr_16799/02_2025/8cqr_16799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqr_16799/02_2025/8cqr_16799.map" model { file = "/net/cci-nas-00/data/ceres_data/8cqr_16799/02_2025/8cqr_16799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqr_16799/02_2025/8cqr_16799.cif" } resolution = 3.8 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= 0.002 sd= 0.009 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 12 5.16 5 C 3138 2.51 5 N 738 2.21 5 O 810 1.98 5 H 5010 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-5592/modules/chem_data/mon_lib" Total number of atoms: 9708 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1618 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "D" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1618 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "A" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1618 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "B" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1618 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "F" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1618 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "C" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1618 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Time building chain proxies: 4.87, per 1000 atoms: 0.50 Number of scatterers: 9708 At special positions: 0 Unit cell: (68.88, 73.8, 118.9, 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 12 16.00 O 810 8.00 N 738 7.00 C 3138 6.00 H 5010 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: 2.49 Conformation dependent library (CDL) restraints added in 793.7 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 84.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'E' and resid 43 through 56 Processing helix chain 'E' and resid 57 through 75 Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 77 through 104 removed outlier: 4.536A pdb=" N VAL E 81 " --> pdb=" O TYR E 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL E 82 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE E 100 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR E 104 " --> pdb=" O PHE E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 138 removed outlier: 3.806A pdb=" N PHE E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 56 Processing helix chain 'D' and resid 57 through 75 Proline residue: D 72 - end of helix Processing helix chain 'D' and resid 77 through 104 removed outlier: 4.535A pdb=" N VAL D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 138 removed outlier: 3.806A pdb=" N PHE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 57 through 75 Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 77 through 104 removed outlier: 4.536A pdb=" N VAL A 81 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 138 removed outlier: 3.806A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 57 through 75 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 77 through 104 removed outlier: 4.536A pdb=" N VAL B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 138 removed outlier: 3.807A pdb=" N PHE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 56 Processing helix chain 'F' and resid 57 through 75 Proline residue: F 72 - end of helix Processing helix chain 'F' and resid 77 through 104 removed outlier: 4.536A pdb=" N VAL F 81 " --> pdb=" O TYR F 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 82 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE F 100 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR F 104 " --> pdb=" O PHE F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 138 removed outlier: 3.806A pdb=" N PHE F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 56 Processing helix chain 'C' and resid 57 through 75 Proline residue: C 72 - end of helix Processing helix chain 'C' and resid 77 through 104 removed outlier: 4.535A pdb=" N VAL C 81 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C 83 " --> pdb=" O PRO C 79 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR C 104 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 138 removed outlier: 3.806A pdb=" N PHE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1098 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: 3.45 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5010 1.03 - 1.23: 0 1.23 - 1.42: 1890 1.42 - 1.61: 2868 1.61 - 1.81: 24 Bond restraints: 9792 Sorted by residual: bond pdb=" CA LYS B 111 " pdb=" C LYS B 111 " ideal model delta sigma weight residual 1.526 1.531 -0.005 1.03e-02 9.43e+03 2.10e-01 bond pdb=" CG PRO A 72 " pdb=" CD PRO A 72 " ideal model delta sigma weight residual 1.503 1.488 0.015 3.40e-02 8.65e+02 2.02e-01 bond pdb=" CA LYS F 111 " pdb=" C LYS F 111 " ideal model delta sigma weight residual 1.526 1.531 -0.005 1.03e-02 9.43e+03 2.00e-01 bond pdb=" CB THR B 123 " pdb=" HB THR B 123 " ideal model delta sigma weight residual 0.970 0.961 0.009 2.00e-02 2.50e+03 1.98e-01 bond pdb=" CG PRO E 72 " pdb=" CD PRO E 72 " ideal model delta sigma weight residual 1.503 1.488 0.015 3.40e-02 8.65e+02 1.92e-01 ... (remaining 9787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.81: 15807 0.81 - 1.61: 1959 1.61 - 2.42: 78 2.42 - 3.23: 1 3.23 - 4.03: 23 Bond angle restraints: 17868 Sorted by residual: angle pdb=" N VAL A 78 " pdb=" CA VAL A 78 " pdb=" C VAL A 78 " ideal model delta sigma weight residual 108.88 112.56 -3.68 2.16e+00 2.14e-01 2.91e+00 angle pdb=" N VAL B 78 " pdb=" CA VAL B 78 " pdb=" C VAL B 78 " ideal model delta sigma weight residual 108.88 112.55 -3.67 2.16e+00 2.14e-01 2.88e+00 angle pdb=" N VAL C 78 " pdb=" CA VAL C 78 " pdb=" C VAL C 78 " ideal model delta sigma weight residual 108.88 112.53 -3.65 2.16e+00 2.14e-01 2.85e+00 angle pdb=" N VAL F 78 " pdb=" CA VAL F 78 " pdb=" C VAL F 78 " ideal model delta sigma weight residual 108.88 112.53 -3.65 2.16e+00 2.14e-01 2.85e+00 angle pdb=" N VAL D 78 " pdb=" CA VAL D 78 " pdb=" C VAL D 78 " ideal model delta sigma weight residual 108.88 112.50 -3.62 2.16e+00 2.14e-01 2.81e+00 ... (remaining 17863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 4238 15.98 - 31.96: 175 31.96 - 47.95: 109 47.95 - 63.93: 32 63.93 - 79.91: 6 Dihedral angle restraints: 4560 sinusoidal: 2436 harmonic: 2124 Sorted by residual: dihedral pdb=" CA VAL E 78 " pdb=" C VAL E 78 " pdb=" N PRO E 79 " pdb=" CA PRO E 79 " ideal model delta harmonic sigma weight residual -180.00 -164.76 -15.24 0 5.00e+00 4.00e-02 9.29e+00 dihedral pdb=" CA VAL B 78 " pdb=" C VAL B 78 " pdb=" N PRO B 79 " pdb=" CA PRO B 79 " ideal model delta harmonic sigma weight residual -180.00 -164.77 -15.23 0 5.00e+00 4.00e-02 9.28e+00 dihedral pdb=" CA VAL C 78 " pdb=" C VAL C 78 " pdb=" N PRO C 79 " pdb=" CA PRO C 79 " ideal model delta harmonic sigma weight residual -180.00 -164.77 -15.23 0 5.00e+00 4.00e-02 9.28e+00 ... (remaining 4557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 526 0.023 - 0.046: 142 0.046 - 0.069: 100 0.069 - 0.092: 58 0.092 - 0.115: 8 Chirality restraints: 834 Sorted by residual: chirality pdb=" CA PRO F 79 " pdb=" N PRO F 79 " pdb=" C PRO F 79 " pdb=" CB PRO F 79 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.30e-01 chirality pdb=" CA PRO C 79 " pdb=" N PRO C 79 " pdb=" C PRO C 79 " pdb=" CB PRO C 79 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.19e-01 chirality pdb=" CA PRO B 79 " pdb=" N PRO B 79 " pdb=" C PRO B 79 " pdb=" CB PRO B 79 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.19e-01 ... (remaining 831 not shown) Planarity restraints: 1386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 78 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO D 79 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 79 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 79 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 78 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO C 79 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 79 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 79 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 78 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO F 79 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 79 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 79 " -0.015 5.00e-02 4.00e+02 ... (remaining 1383 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1119 2.26 - 2.84: 23046 2.84 - 3.43: 24341 3.43 - 4.01: 30756 4.01 - 4.60: 49618 Nonbonded interactions: 128880 Sorted by model distance: nonbonded pdb=" O GLU F 69 " pdb=" HG SER F 73 " model vdw 1.674 2.450 nonbonded pdb=" O GLU E 69 " pdb=" HG SER E 73 " model vdw 1.674 2.450 nonbonded pdb=" O GLU D 69 " pdb=" HG SER D 73 " model vdw 1.675 2.450 nonbonded pdb=" O GLU C 69 " pdb=" HG SER C 73 " model vdw 1.688 2.450 nonbonded pdb=" O GLU B 69 " pdb=" HG SER B 73 " model vdw 1.689 2.450 ... (remaining 128875 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 1.400 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: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 23.180 Find NCS groups from input model: 0.130 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 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 : 0.002 0.017 4782 Z= 0.128 Angle : 0.425 4.032 6510 Z= 0.231 Chirality : 0.035 0.115 834 Planarity : 0.003 0.027 792 Dihedral : 11.296 79.912 1656 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % 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: 0.53 (0.32), residues: 606 helix: 1.63 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -3.71 (0.29), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 112 PHE 0.009 0.001 PHE F 135 TYR 0.002 0.000 TYR D 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 THR cc_start: 0.8954 (p) cc_final: 0.8608 (p) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2691 time to fit residues: 58.2128 Evaluate side-chains 83 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 HIS A 70 GLN A 91 GLN B 91 GLN C 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.163485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.149092 restraints weight = 45060.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.153254 restraints weight = 22640.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.155751 restraints weight = 13549.474| |-----------------------------------------------------------------------------| r_work (final): 0.4714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4782 Z= 0.189 Angle : 0.580 6.622 6510 Z= 0.314 Chirality : 0.038 0.124 834 Planarity : 0.003 0.024 792 Dihedral : 3.581 15.879 630 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.91 % Allowed : 19.19 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.34), residues: 606 helix: 2.17 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -3.27 (0.38), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 40 PHE 0.015 0.001 PHE D 127 TYR 0.010 0.001 TYR B 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 ILE cc_start: 0.9087 (mt) cc_final: 0.8842 (mt) REVERT: C 133 ASN cc_start: 0.7531 (m110) cc_final: 0.7217 (m110) outliers start: 15 outliers final: 9 residues processed: 106 average time/residue: 0.2835 time to fit residues: 40.0370 Evaluate side-chains 86 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN C 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.152874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.134919 restraints weight = 45544.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.140631 restraints weight = 19567.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.144158 restraints weight = 10575.089| |-----------------------------------------------------------------------------| r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4782 Z= 0.201 Angle : 0.561 4.868 6510 Z= 0.306 Chirality : 0.037 0.121 834 Planarity : 0.003 0.027 792 Dihedral : 3.537 15.025 630 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.71 % Allowed : 18.99 % Favored : 78.29 % 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: 1.12 (0.35), residues: 606 helix: 1.82 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -3.24 (0.43), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 40 PHE 0.015 0.001 PHE A 117 TYR 0.006 0.001 TYR E 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.5229 (ppp) cc_final: 0.4970 (mtt) REVERT: C 111 LYS cc_start: 0.3450 (pttt) cc_final: 0.2299 (pptt) REVERT: C 129 ILE cc_start: 0.8959 (mt) cc_final: 0.8721 (mt) REVERT: C 133 ASN cc_start: 0.8079 (m110) cc_final: 0.7688 (m110) outliers start: 14 outliers final: 12 residues processed: 102 average time/residue: 0.2909 time to fit residues: 39.5795 Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain C residue 100 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN B 133 ASN C 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.161193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.146634 restraints weight = 35593.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.151560 restraints weight = 13295.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.154466 restraints weight = 6495.843| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4782 Z= 0.178 Angle : 0.549 7.535 6510 Z= 0.293 Chirality : 0.036 0.118 834 Planarity : 0.003 0.026 792 Dihedral : 3.526 14.868 630 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.52 % Allowed : 18.60 % Favored : 78.88 % 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: 0.87 (0.35), residues: 606 helix: 1.85 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -4.21 (0.36), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.013 0.001 PHE C 117 TYR 0.005 0.001 TYR C 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8852 (mm-30) outliers start: 13 outliers final: 10 residues processed: 99 average time/residue: 0.2905 time to fit residues: 39.2830 Evaluate side-chains 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 55 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.163074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.148317 restraints weight = 35799.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.153140 restraints weight = 14479.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.156229 restraints weight = 7478.594| |-----------------------------------------------------------------------------| r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4782 Z= 0.143 Angle : 0.530 6.162 6510 Z= 0.280 Chirality : 0.036 0.123 834 Planarity : 0.003 0.025 792 Dihedral : 3.385 14.219 630 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.94 % Allowed : 19.57 % Favored : 78.49 % 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: 1.16 (0.35), residues: 606 helix: 2.16 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -4.22 (0.36), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.008 0.001 PHE A 135 TYR 0.005 0.001 TYR C 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8821 (mm-30) REVERT: A 129 ILE cc_start: 0.9022 (mt) cc_final: 0.8818 (mt) REVERT: A 133 ASN cc_start: 0.7946 (m-40) cc_final: 0.7591 (m110) REVERT: B 70 GLN cc_start: 0.7808 (mt0) cc_final: 0.7563 (pt0) REVERT: C 51 MET cc_start: 0.7327 (tmm) cc_final: 0.6993 (tmm) REVERT: C 129 ILE cc_start: 0.9215 (mt) cc_final: 0.8533 (mt) REVERT: C 133 ASN cc_start: 0.8016 (m-40) cc_final: 0.7288 (m110) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 0.2520 time to fit residues: 36.9732 Evaluate side-chains 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.159424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.144690 restraints weight = 36106.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.149455 restraints weight = 14196.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.152616 restraints weight = 7285.109| |-----------------------------------------------------------------------------| r_work (final): 0.4597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4782 Z= 0.231 Angle : 0.604 7.468 6510 Z= 0.327 Chirality : 0.037 0.125 834 Planarity : 0.003 0.027 792 Dihedral : 3.710 14.376 630 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.10 % Allowed : 19.38 % Favored : 77.52 % 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: 0.46 (0.34), residues: 606 helix: 1.52 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -4.24 (0.37), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 40 PHE 0.018 0.002 PHE A 135 TYR 0.005 0.001 TYR F 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8960 (mm-30) REVERT: B 70 GLN cc_start: 0.8196 (mt0) cc_final: 0.7763 (pt0) REVERT: C 51 MET cc_start: 0.7388 (tmm) cc_final: 0.7088 (tmm) REVERT: C 133 ASN cc_start: 0.8308 (m-40) cc_final: 0.7787 (m110) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.2593 time to fit residues: 35.4676 Evaluate side-chains 97 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 120 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.160968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.146038 restraints weight = 35904.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.151354 restraints weight = 13112.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.154690 restraints weight = 6289.007| |-----------------------------------------------------------------------------| r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4782 Z= 0.153 Angle : 0.533 6.368 6510 Z= 0.283 Chirality : 0.036 0.115 834 Planarity : 0.003 0.025 792 Dihedral : 3.466 13.615 630 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.94 % Allowed : 20.74 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.35), residues: 606 helix: 1.98 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -4.22 (0.36), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.015 0.001 PHE B 117 TYR 0.004 0.001 TYR B 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.3749 (mtt) cc_final: 0.3089 (ttt) REVERT: C 51 MET cc_start: 0.7277 (tmm) cc_final: 0.7057 (tmm) REVERT: C 129 ILE cc_start: 0.9064 (mt) cc_final: 0.8705 (mt) REVERT: C 133 ASN cc_start: 0.8300 (m-40) cc_final: 0.7779 (m110) outliers start: 10 outliers final: 9 residues processed: 104 average time/residue: 0.2468 time to fit residues: 35.6379 Evaluate side-chains 98 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.160786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.144829 restraints weight = 36572.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.150634 restraints weight = 13446.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.154145 restraints weight = 6478.990| |-----------------------------------------------------------------------------| r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4782 Z= 0.158 Angle : 0.538 6.960 6510 Z= 0.287 Chirality : 0.037 0.146 834 Planarity : 0.003 0.025 792 Dihedral : 3.403 13.974 630 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.94 % Allowed : 21.51 % Favored : 76.55 % 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: 1.03 (0.35), residues: 606 helix: 2.05 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -4.24 (0.36), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.018 0.001 PHE A 117 TYR 0.004 0.001 TYR C 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.3781 (mtt) cc_final: 0.3144 (ttt) REVERT: B 70 GLN cc_start: 0.8262 (mt0) cc_final: 0.7871 (pt0) REVERT: C 51 MET cc_start: 0.7313 (tmm) cc_final: 0.7037 (tmm) REVERT: C 129 ILE cc_start: 0.9104 (mt) cc_final: 0.8729 (mt) REVERT: C 133 ASN cc_start: 0.8284 (m-40) cc_final: 0.7776 (m110) outliers start: 10 outliers final: 9 residues processed: 103 average time/residue: 0.2616 time to fit residues: 37.2129 Evaluate side-chains 102 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 0.0270 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.162233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.147446 restraints weight = 35717.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.152783 restraints weight = 13209.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.156038 restraints weight = 6303.876| |-----------------------------------------------------------------------------| r_work (final): 0.4765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.6952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4782 Z= 0.143 Angle : 0.534 9.020 6510 Z= 0.278 Chirality : 0.036 0.136 834 Planarity : 0.003 0.026 792 Dihedral : 3.268 12.959 630 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.94 % Allowed : 21.51 % Favored : 76.55 % 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: 1.27 (0.36), residues: 606 helix: 2.25 (0.25), residues: 462 sheet: None (None), residues: 0 loop : -4.28 (0.36), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.018 0.001 PHE B 117 TYR 0.004 0.001 TYR C 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.3698 (mtt) cc_final: 0.3037 (ttt) REVERT: A 70 GLN cc_start: 0.8505 (mt0) cc_final: 0.8300 (mt0) REVERT: B 70 GLN cc_start: 0.8423 (mt0) cc_final: 0.7986 (pt0) REVERT: C 51 MET cc_start: 0.7230 (tmm) cc_final: 0.6918 (tmm) REVERT: C 129 ILE cc_start: 0.8986 (mt) cc_final: 0.8621 (mt) REVERT: C 133 ASN cc_start: 0.8290 (m-40) cc_final: 0.7771 (m110) outliers start: 10 outliers final: 10 residues processed: 106 average time/residue: 0.2484 time to fit residues: 37.0115 Evaluate side-chains 104 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.4592 r_free = 0.4592 target = 0.149730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.133320 restraints weight = 43260.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.138866 restraints weight = 18328.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.142275 restraints weight = 9804.237| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.7216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4782 Z= 0.194 Angle : 0.581 8.834 6510 Z= 0.309 Chirality : 0.037 0.137 834 Planarity : 0.003 0.025 792 Dihedral : 3.394 13.418 630 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.94 % Allowed : 21.90 % Favored : 76.16 % 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: 0.88 (0.36), residues: 606 helix: 1.88 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -4.32 (0.37), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.019 0.002 PHE B 135 TYR 0.004 0.001 TYR E 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.3696 (mtt) cc_final: 0.2921 (ttt) REVERT: B 70 GLN cc_start: 0.8356 (mt0) cc_final: 0.7831 (pt0) REVERT: C 51 MET cc_start: 0.7219 (tmm) cc_final: 0.6958 (tmm) REVERT: C 129 ILE cc_start: 0.9102 (mt) cc_final: 0.8733 (mt) REVERT: C 133 ASN cc_start: 0.8305 (m-40) cc_final: 0.7789 (m110) outliers start: 10 outliers final: 10 residues processed: 101 average time/residue: 0.2610 time to fit residues: 36.9298 Evaluate side-chains 99 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.162776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.147756 restraints weight = 36115.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.153086 restraints weight = 13427.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.156483 restraints weight = 6528.745| |-----------------------------------------------------------------------------| r_work (final): 0.4669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.7281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4782 Z= 0.149 Angle : 0.541 8.583 6510 Z= 0.281 Chirality : 0.036 0.116 834 Planarity : 0.003 0.025 792 Dihedral : 3.286 12.943 630 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.94 % Allowed : 21.51 % Favored : 76.55 % 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: 1.13 (0.36), residues: 606 helix: 2.16 (0.25), residues: 462 sheet: None (None), residues: 0 loop : -4.34 (0.36), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.017 0.001 PHE B 117 TYR 0.004 0.001 TYR C 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.28 seconds wall clock time: 53 minutes 20.08 seconds (3200.08 seconds total)