Starting phenix.real_space_refine on Fri Mar 14 06:24:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqr_16799/03_2025/8cqr_16799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqr_16799/03_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_16799/03_2025/8cqr_16799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqr_16799/03_2025/8cqr_16799.map" model { file = "/net/cci-nas-00/data/ceres_data/8cqr_16799/03_2025/8cqr_16799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqr_16799/03_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-5624/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: 4.80, per 1000 atoms: 0.49 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: 2.26 Conformation dependent library (CDL) restraints added in 747.0 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: 0.59 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: 3.12 Time building geometry restraints manager: 2.81 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: 0.05 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: 1.940 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: 0.170 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.610 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- 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 : 0.701 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: 0.2577 time to fit residues: 55.4553 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 : 0.658 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.149087 restraints weight = 45060.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.153170 restraints weight = 22643.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.155831 restraints weight = 13707.421| |-----------------------------------------------------------------------------| r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 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 : 0.712 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: 0.9091 (mt) cc_final: 0.8846 (mt) REVERT: C 133 ASN cc_start: 0.7548 (m110) cc_final: 0.7230 (m110) outliers start: 15 outliers final: 9 residues processed: 106 average time/residue: 0.2856 time to fit residues: 40.5143 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 : 0.760 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.7980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4789 r_free = 0.4789 target = 0.160236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.146587 restraints weight = 45698.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.150602 restraints weight = 22553.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.153223 restraints weight = 13395.494| |-----------------------------------------------------------------------------| r_work (final): 0.4695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4782 Z= 0.179 Angle : 0.543 4.850 6510 Z= 0.295 Chirality : 0.037 0.119 834 Planarity : 0.003 0.026 792 Dihedral : 3.461 15.002 630 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.13 % Allowed : 19.38 % 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: 1.30 (0.35), residues: 606 helix: 1.96 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -3.24 (0.42), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 112 PHE 0.017 0.001 PHE A 117 TYR 0.007 0.001 TYR B 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 101 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.668 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: B 70 GLN cc_start: 0.7822 (mt0) cc_final: 0.7573 (pt0) REVERT: C 51 MET cc_start: 0.7320 (mmm) cc_final: 0.7092 (mmm) REVERT: C 111 LYS cc_start: 0.2640 (pttt) cc_final: 0.1710 (pptt) REVERT: C 129 ILE cc_start: 0.9113 (mt) cc_final: 0.8874 (mt) REVERT: C 133 ASN cc_start: 0.7745 (m110) cc_final: 0.7386 (m110) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.2817 time to fit residues: 37.5341 Evaluate side-chains 92 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 115 LEU Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.158653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.144143 restraints weight = 35927.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.148868 restraints weight = 13652.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.151896 restraints weight = 6773.080| |-----------------------------------------------------------------------------| r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4782 Z= 0.259 Angle : 0.615 6.947 6510 Z= 0.336 Chirality : 0.038 0.124 834 Planarity : 0.003 0.028 792 Dihedral : 3.862 14.774 630 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.49 % Allowed : 18.80 % Favored : 77.71 % 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: 0.63 (0.34), residues: 606 helix: 1.41 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -4.19 (0.43), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 40 PHE 0.016 0.002 PHE A 135 TYR 0.007 0.001 TYR F 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 106 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.802 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: E 103 LYS cc_start: 0.7305 (mmtt) cc_final: 0.7103 (mttm) REVERT: D 49 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8906 (mm-30) REVERT: B 70 GLN cc_start: 0.8124 (mt0) cc_final: 0.7899 (mt0) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.3083 time to fit residues: 44.4922 Evaluate side-chains 95 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 D residue 128 ILE 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 Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 0.0670 overall best weight: 1.7322 ------------------------------------------------------------------------------- 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 C 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.158806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.140278 restraints weight = 43899.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.145926 restraints weight = 19204.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.148867 restraints weight = 10646.682| |-----------------------------------------------------------------------------| r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4782 Z= 0.163 Angle : 0.534 5.446 6510 Z= 0.288 Chirality : 0.036 0.117 834 Planarity : 0.003 0.027 792 Dihedral : 3.646 13.977 630 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: 0.80 (0.35), residues: 606 helix: 1.84 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -4.15 (0.36), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 40 PHE 0.014 0.001 PHE A 117 TYR 0.004 0.001 TYR B 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 110 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.756 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: D 49 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9065 (mm-30) REVERT: B 70 GLN cc_start: 0.8651 (mt0) cc_final: 0.8404 (mt0) REVERT: B 133 ASN cc_start: 0.8187 (m-40) cc_final: 0.7617 (m110) outliers start: 15 outliers final: 13 residues processed: 110 average time/residue: 0.2589 time to fit residues: 39.1960 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 : 0.740 ------------------------------------------------------------------------------- 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 D residue 118 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain B residue 87 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 = 0.4720 r_free = 0.4720 target = 0.161073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.146638 restraints weight = 36327.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.151441 restraints weight = 13861.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.154686 restraints weight = 6978.442| |-----------------------------------------------------------------------------| r_work (final): 0.4676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.6435 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= 0.161 Angle : 0.532 6.196 6510 Z= 0.285 Chirality : 0.037 0.140 834 Planarity : 0.003 0.029 792 Dihedral : 3.549 14.172 630 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.52 % Allowed : 19.96 % 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: 0.96 (0.35), residues: 606 helix: 1.97 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -4.14 (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 C 117 TYR 0.004 0.001 TYR C 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 107 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.705 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: 0.9158 (mm-30) cc_final: 0.8942 (mm-30) REVERT: B 70 GLN cc_start: 0.8134 (mt0) cc_final: 0.7871 (mt0) REVERT: B 133 ASN cc_start: 0.8105 (m-40) cc_final: 0.7520 (m110) REVERT: C 129 ILE cc_start: 0.9030 (mt) cc_final: 0.8703 (mt) REVERT: C 133 ASN cc_start: 0.8152 (m-40) cc_final: 0.7593 (m110) outliers start: 13 outliers final: 10 residues processed: 107 average time/residue: 0.2545 time to fit residues: 37.7092 Evaluate side-chains 101 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A 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 87 SER Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 C 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.161560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.146767 restraints weight = 36061.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.152088 restraints weight = 13085.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.155459 restraints weight = 6299.902| |-----------------------------------------------------------------------------| r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.6629 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= 0.149 Angle : 0.531 8.497 6510 Z= 0.279 Chirality : 0.037 0.138 834 Planarity : 0.003 0.029 792 Dihedral : 3.438 13.616 630 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.13 % Allowed : 21.12 % Favored : 76.74 % 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: 1.14 (0.36), residues: 606 helix: 2.12 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -4.14 (0.37), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.017 0.001 PHE A 117 TYR 0.004 0.001 TYR C 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 108 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.687 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: symmetry clash REVERT: A 51 MET cc_start: 0.3657 (mtt) cc_final: 0.3042 (ttt) REVERT: B 70 GLN cc_start: 0.8084 (mt0) cc_final: 0.7817 (mt0) REVERT: C 58 MET cc_start: 0.8486 (mpp) cc_final: 0.7545 (tpt) REVERT: C 129 ILE cc_start: 0.9035 (mt) cc_final: 0.8698 (mt) REVERT: C 133 ASN cc_start: 0.8137 (m-40) cc_final: 0.7577 (m110) outliers start: 11 outliers final: 10 residues processed: 108 average time/residue: 0.2682 time to fit residues: 39.6311 Evaluate side-chains 101 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN C 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.160532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.145944 restraints weight = 36130.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.151163 restraints weight = 12985.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.154373 restraints weight = 6219.560| |-----------------------------------------------------------------------------| r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4782 Z= 0.186 Angle : 0.557 7.457 6510 Z= 0.300 Chirality : 0.037 0.146 834 Planarity : 0.003 0.027 792 Dihedral : 3.528 13.773 630 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.71 % Allowed : 21.12 % 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: 0.80 (0.35), residues: 606 helix: 1.79 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -4.19 (0.38), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 40 PHE 0.016 0.001 PHE A 135 TYR 0.004 0.001 TYR F 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: 14 poor density : 91 time to evaluate : 0.682 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: B 70 GLN cc_start: 0.8456 (mt0) cc_final: 0.8180 (mt0) REVERT: C 49 GLU cc_start: 0.7730 (tp30) cc_final: 0.6871 (pp20) REVERT: C 58 MET cc_start: 0.8835 (mpp) cc_final: 0.7711 (tpt) REVERT: C 129 ILE cc_start: 0.8844 (mt) cc_final: 0.8557 (mt) REVERT: C 133 ASN cc_start: 0.8313 (m-40) cc_final: 0.7739 (m110) outliers start: 14 outliers final: 13 residues processed: 105 average time/residue: 0.2583 time to fit residues: 37.4168 Evaluate side-chains 102 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 115 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.163039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.148322 restraints weight = 36067.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.153558 restraints weight = 13261.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.156906 restraints weight = 6385.433| |-----------------------------------------------------------------------------| r_work (final): 0.4783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.7039 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= 0.142 Angle : 0.527 8.730 6510 Z= 0.277 Chirality : 0.036 0.148 834 Planarity : 0.003 0.028 792 Dihedral : 3.350 13.033 630 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.13 % Allowed : 22.29 % Favored : 75.58 % 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: 1.24 (0.36), residues: 606 helix: 2.21 (0.25), residues: 462 sheet: None (None), residues: 0 loop : -4.21 (0.37), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.021 0.001 PHE A 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: 11 poor density : 96 time to evaluate : 0.772 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: symmetry clash REVERT: D 104 TYR cc_start: 0.5752 (t80) cc_final: 0.5537 (t80) REVERT: A 51 MET cc_start: 0.3627 (mtt) cc_final: 0.2898 (ttt) REVERT: A 70 GLN cc_start: 0.8527 (mt0) cc_final: 0.8320 (mt0) REVERT: B 70 GLN cc_start: 0.8424 (mt0) cc_final: 0.8134 (mt0) REVERT: C 129 ILE cc_start: 0.8844 (mt) cc_final: 0.8562 (mt) REVERT: C 133 ASN cc_start: 0.8281 (m-40) cc_final: 0.7712 (m110) outliers start: 11 outliers final: 11 residues processed: 105 average time/residue: 0.2575 time to fit residues: 37.2514 Evaluate side-chains 104 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 116 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4694 r_free = 0.4694 target = 0.160235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.145759 restraints weight = 36229.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.150945 restraints weight = 13032.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.154208 restraints weight = 6237.510| |-----------------------------------------------------------------------------| r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.7296 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= 0.199 Angle : 0.565 8.268 6510 Z= 0.305 Chirality : 0.036 0.148 834 Planarity : 0.003 0.027 792 Dihedral : 3.507 13.564 630 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.94 % Allowed : 22.48 % Favored : 75.58 % 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: 0.79 (0.35), residues: 606 helix: 1.79 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -4.24 (0.38), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 40 PHE 0.018 0.001 PHE A 135 TYR 0.004 0.001 TYR A 77 ********************** 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 97 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.668 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: C 58 MET cc_start: 0.8777 (mpp) cc_final: 0.7682 (tpt) REVERT: C 129 ILE cc_start: 0.8833 (mt) cc_final: 0.8550 (mt) REVERT: C 133 ASN cc_start: 0.8305 (m-40) cc_final: 0.7736 (m110) outliers start: 10 outliers final: 9 residues processed: 96 average time/residue: 0.2388 time to fit residues: 32.1267 Evaluate side-chains 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain A residue 135 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4706 r_free = 0.4706 target = 0.161211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.146972 restraints weight = 35763.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.151954 restraints weight = 13179.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.155188 restraints weight = 6399.094| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.7370 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= 0.164 Angle : 0.541 8.564 6510 Z= 0.288 Chirality : 0.036 0.141 834 Planarity : 0.003 0.027 792 Dihedral : 3.450 13.494 630 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.33 % Allowed : 22.09 % Favored : 75.58 % 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: 0.90 (0.36), residues: 606 helix: 1.89 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -4.28 (0.38), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.014 0.001 PHE B 117 TYR 0.004 0.001 TYR B 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.47 seconds wall clock time: 54 minutes 7.68 seconds (3247.68 seconds total)