Starting phenix.real_space_refine on Thu Mar 14 20:08:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqr_16799/03_2024/8cqr_16799.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqr_16799/03_2024/8cqr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqr_16799/03_2024/8cqr_16799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqr_16799/03_2024/8cqr_16799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqr_16799/03_2024/8cqr_16799.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqr_16799/03_2024/8cqr_16799.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.44, per 1000 atoms: 0.46 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 - 3.50 Amino acid : False - 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: 7.58 Conformation dependent library (CDL) restraints added in 967.7 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: 0.60 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: 3.05 Time building geometry restraints manager: 7.88 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: 100.90 - 106.97: 112 106.97 - 113.03: 12126 113.03 - 119.09: 1742 119.09 - 125.15: 3769 125.15 - 131.21: 119 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 1.850 nonbonded pdb=" O GLU E 69 " pdb=" HG SER E 73 " model vdw 1.674 1.850 nonbonded pdb=" O GLU D 69 " pdb=" HG SER D 73 " model vdw 1.675 1.850 nonbonded pdb=" O GLU C 69 " pdb=" HG SER C 73 " model vdw 1.688 1.850 nonbonded pdb=" O GLU B 69 " pdb=" HG SER B 73 " model vdw 1.689 1.850 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 1.060 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: 0.150 Extract box with map and model: 5.890 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.520 Find NCS groups from input model: 0.400 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.787 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: 0.2610 time to fit residues: 56.2005 Evaluate side-chains 83 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 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 70 GLN A 91 GLN B 91 GLN C 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.3801 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= 0.187 Angle : 0.572 6.545 6510 Z= 0.313 Chirality : 0.038 0.124 834 Planarity : 0.003 0.024 792 Dihedral : 3.625 15.912 630 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.07 % Allowed : 18.02 % 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: 1.35 (0.34), residues: 606 helix: 2.03 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -3.34 (0.40), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 40 PHE 0.016 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 114 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.811 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: C 129 ILE cc_start: 0.8936 (mt) cc_final: 0.8689 (mt) REVERT: C 133 ASN cc_start: 0.8018 (m110) cc_final: 0.7620 (m110) outliers start: 21 outliers final: 14 residues processed: 112 average time/residue: 0.2848 time to fit residues: 42.8660 Evaluate side-chains 94 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 60 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 60 ASN 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 58 MET Chi-restraints excluded: chain C residue 60 ASN 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 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 70 GLN C 70 GLN C 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4782 Z= 0.145 Angle : 0.507 4.341 6510 Z= 0.274 Chirality : 0.036 0.117 834 Planarity : 0.003 0.025 792 Dihedral : 3.402 14.941 630 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.74 % Allowed : 19.57 % Favored : 78.68 % 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: 1.67 (0.35), residues: 606 helix: 2.40 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -3.32 (0.39), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 112 PHE 0.014 0.001 PHE A 117 TYR 0.007 0.001 TYR C 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 109 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.628 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: B 70 GLN cc_start: 0.8508 (mt0) cc_final: 0.8220 (pt0) REVERT: C 129 ILE cc_start: 0.8933 (mt) cc_final: 0.8696 (mt) REVERT: C 133 ASN cc_start: 0.7963 (m-40) cc_final: 0.7560 (m110) outliers start: 9 outliers final: 7 residues processed: 108 average time/residue: 0.2843 time to fit residues: 40.8040 Evaluate side-chains 95 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 100 PHE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.5319 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= 0.186 Angle : 0.541 6.946 6510 Z= 0.293 Chirality : 0.036 0.120 834 Planarity : 0.003 0.026 792 Dihedral : 3.536 15.045 630 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.91 % Allowed : 18.99 % Favored : 78.10 % 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: 1.32 (0.35), residues: 606 helix: 1.99 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -4.14 (0.41), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.015 0.001 PHE C 117 TYR 0.005 0.001 TYR D 77 *********************** 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 103 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.814 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 129 ILE cc_start: 0.8824 (mt) cc_final: 0.8582 (mt) REVERT: C 111 LYS cc_start: 0.3496 (pttt) cc_final: 0.2337 (pptt) REVERT: C 129 ILE cc_start: 0.8975 (mt) cc_final: 0.8634 (mt) REVERT: C 133 ASN cc_start: 0.8155 (m-40) cc_final: 0.7661 (m110) outliers start: 15 outliers final: 15 residues processed: 100 average time/residue: 0.2821 time to fit residues: 38.0130 Evaluate side-chains 96 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 58 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 87 SER 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 0 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4782 Z= 0.150 Angle : 0.505 5.407 6510 Z= 0.272 Chirality : 0.035 0.120 834 Planarity : 0.003 0.028 792 Dihedral : 3.394 14.181 630 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.71 % Allowed : 20.54 % 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: 1.53 (0.35), residues: 606 helix: 2.23 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -4.19 (0.39), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 40 PHE 0.018 0.001 PHE B 117 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 103 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.620 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: D 49 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9063 (mm-30) REVERT: B 70 GLN cc_start: 0.8546 (mt0) cc_final: 0.8111 (pt0) REVERT: C 129 ILE cc_start: 0.8964 (mt) cc_final: 0.8608 (mt) REVERT: C 133 ASN cc_start: 0.8090 (m-40) cc_final: 0.7583 (m110) outliers start: 14 outliers final: 13 residues processed: 102 average time/residue: 0.2688 time to fit residues: 36.9536 Evaluate side-chains 95 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 87 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 115 LEU 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 C residue 58 MET Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.6076 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= 0.147 Angle : 0.502 4.505 6510 Z= 0.270 Chirality : 0.036 0.130 834 Planarity : 0.003 0.028 792 Dihedral : 3.402 14.217 630 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.91 % Allowed : 20.74 % Favored : 76.36 % 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: 1.56 (0.35), residues: 606 helix: 2.26 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -4.20 (0.40), residues: 126 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 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 106 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.775 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: 0.9299 (mm-30) cc_final: 0.9058 (mm-30) REVERT: A 139 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6642 (t80) REVERT: B 70 GLN cc_start: 0.8567 (mt0) cc_final: 0.8090 (pt0) REVERT: C 129 ILE cc_start: 0.8895 (mt) cc_final: 0.8669 (mt) REVERT: C 133 ASN cc_start: 0.8098 (m-40) cc_final: 0.7633 (m110) outliers start: 15 outliers final: 14 residues processed: 104 average time/residue: 0.2649 time to fit residues: 38.2185 Evaluate side-chains 102 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 129 ILE 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 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 C residue 58 MET 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 32 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.6407 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= 0.132 Angle : 0.499 8.346 6510 Z= 0.265 Chirality : 0.036 0.129 834 Planarity : 0.003 0.027 792 Dihedral : 3.293 13.542 630 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.33 % Allowed : 21.71 % Favored : 75.97 % 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: 1.76 (0.36), residues: 606 helix: 2.41 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -4.21 (0.41), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 40 PHE 0.020 0.001 PHE C 117 TYR 0.006 0.001 TYR E 77 *********************** 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 fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.737 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 49 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9062 (mm-30) REVERT: A 139 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6579 (t80) REVERT: C 129 ILE cc_start: 0.8895 (mt) cc_final: 0.8651 (mt) REVERT: C 133 ASN cc_start: 0.8046 (m-40) cc_final: 0.7560 (m110) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.2547 time to fit residues: 37.1658 Evaluate side-chains 100 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 100 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 28 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 B 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4782 Z= 0.137 Angle : 0.499 7.367 6510 Z= 0.267 Chirality : 0.036 0.158 834 Planarity : 0.003 0.027 792 Dihedral : 3.221 13.888 630 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.71 % Allowed : 21.32 % Favored : 75.97 % 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: 1.85 (0.36), residues: 606 helix: 2.48 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -4.20 (0.41), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 40 PHE 0.018 0.001 PHE C 117 TYR 0.005 0.001 TYR E 77 *********************** 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 107 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.845 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 49 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9081 (mm-30) REVERT: A 139 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.6613 (t80) REVERT: B 70 GLN cc_start: 0.8425 (mt0) cc_final: 0.8167 (pt0) REVERT: C 129 ILE cc_start: 0.8904 (mt) cc_final: 0.8659 (mt) REVERT: C 133 ASN cc_start: 0.8093 (m-40) cc_final: 0.7610 (m110) outliers start: 14 outliers final: 11 residues processed: 105 average time/residue: 0.2768 time to fit residues: 39.4745 Evaluate side-chains 102 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4782 Z= 0.132 Angle : 0.493 7.102 6510 Z= 0.263 Chirality : 0.036 0.143 834 Planarity : 0.003 0.027 792 Dihedral : 3.158 13.048 630 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.52 % Allowed : 21.71 % Favored : 75.78 % 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: 1.92 (0.36), residues: 606 helix: 2.55 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -4.25 (0.41), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 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 110 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.719 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 139 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6628 (t80) REVERT: B 70 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: C 129 ILE cc_start: 0.8900 (mt) cc_final: 0.8653 (mt) REVERT: C 133 ASN cc_start: 0.8087 (m-40) cc_final: 0.7599 (m110) outliers start: 13 outliers final: 10 residues processed: 107 average time/residue: 0.2650 time to fit residues: 38.6187 Evaluate side-chains 103 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 100 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain B residue 70 GLN 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 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 43 optimal weight: 0.1980 chunk 7 optimal weight: 0.0670 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.2716 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.6823 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= 0.134 Angle : 0.507 9.436 6510 Z= 0.268 Chirality : 0.036 0.161 834 Planarity : 0.003 0.028 792 Dihedral : 3.131 13.283 630 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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: 1.99 (0.36), residues: 606 helix: 2.60 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -4.26 (0.41), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 40 PHE 0.019 0.001 PHE C 117 TYR 0.004 0.000 TYR C 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 103 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.788 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 139 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6545 (t80) REVERT: C 129 ILE cc_start: 0.8900 (mt) cc_final: 0.8655 (mt) REVERT: C 133 ASN cc_start: 0.8057 (m-40) cc_final: 0.7571 (m110) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.2671 time to fit residues: 37.2906 Evaluate side-chains 99 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.161584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.146637 restraints weight = 35920.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.152198 restraints weight = 13519.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.155398 restraints weight = 6467.203| |-----------------------------------------------------------------------------| r_work (final): 0.4770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4782 Z= 0.157 Angle : 0.518 8.255 6510 Z= 0.279 Chirality : 0.035 0.116 834 Planarity : 0.003 0.026 792 Dihedral : 3.164 12.624 630 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.33 % Allowed : 22.29 % Favored : 75.39 % 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: 1.86 (0.36), residues: 606 helix: 2.41 (0.24), residues: 486 sheet: None (None), residues: 0 loop : -4.14 (0.42), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 40 PHE 0.016 0.001 PHE E 76 TYR 0.003 0.001 TYR E 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.23 seconds wall clock time: 43 minutes 27.01 seconds (2607.01 seconds total)