Starting phenix.real_space_refine on Sat Aug 23 04:18:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqr_16799/08_2025/8cqr_16799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqr_16799/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8cqr_16799/08_2025/8cqr_16799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqr_16799/08_2025/8cqr_16799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cqr_16799/08_2025/8cqr_16799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqr_16799/08_2025/8cqr_16799.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.74, per 1000 atoms: 0.18 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: 0.56 Conformation dependent library (CDL) restraints added in 253.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 1.87 Time building geometry restraints manager: 0.88 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: 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: 0.02 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'C' } 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.490 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.670 ------------------------------------------------------------------------------- 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= 0.087 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (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 TYR 0.002 0.000 TYR D 104 PHE 0.009 0.001 PHE F 135 HIS 0.001 0.000 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 4782) covalent geometry : angle 0.42504 ( 6510) hydrogen bonds : bond 0.19069 ( 366) hydrogen bonds : angle 6.54244 ( 1098) *********************** 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 : 0.267 Fit side-chains 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: 0.8628 (p) REVERT: C 70 GLN cc_start: 0.8913 (mt0) cc_final: 0.8653 (pt0) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1199 time to fit residues: 26.2994 Evaluate side-chains 84 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN B 91 GLN C 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.164680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.149309 restraints weight = 44284.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.153833 restraints weight = 21324.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.156742 restraints weight = 12655.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.158591 restraints weight = 8201.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.159976 restraints weight = 5835.411| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4782 Z= 0.127 Angle : 0.569 7.230 6510 Z= 0.302 Chirality : 0.038 0.121 834 Planarity : 0.003 0.022 792 Dihedral : 3.490 15.816 630 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.52 % Allowed : 19.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.35), residues: 606 helix: 2.35 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -3.43 (0.36), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR E 104 PHE 0.015 0.001 PHE D 127 HIS 0.002 0.000 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4782) covalent geometry : angle 0.56920 ( 6510) hydrogen bonds : bond 0.04858 ( 366) hydrogen bonds : angle 3.88963 ( 1098) *********************** 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 113 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.196 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 129 ILE cc_start: 0.9069 (mt) cc_final: 0.8828 (mt) REVERT: C 133 ASN cc_start: 0.7671 (m110) cc_final: 0.7335 (m110) outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 0.1065 time to fit residues: 16.0155 Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 87 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 0.0270 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.0050 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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 = 0.4838 r_free = 0.4838 target = 0.164937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.150777 restraints weight = 44433.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.154921 restraints weight = 22522.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.157586 restraints weight = 13542.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.159388 restraints weight = 8932.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.160718 restraints weight = 6280.296| |-----------------------------------------------------------------------------| r_work (final): 0.4765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4782 Z= 0.113 Angle : 0.526 8.156 6510 Z= 0.275 Chirality : 0.036 0.116 834 Planarity : 0.003 0.024 792 Dihedral : 3.311 14.919 630 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.55 % Allowed : 20.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.35), residues: 606 helix: 2.48 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -3.36 (0.38), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.000 TYR A 104 PHE 0.017 0.001 PHE A 117 HIS 0.004 0.000 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4782) covalent geometry : angle 0.52576 ( 6510) hydrogen bonds : bond 0.04022 ( 366) hydrogen bonds : angle 3.56638 ( 1098) *********************** 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 118 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.263 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 GLN cc_start: 0.7678 (mt0) cc_final: 0.7441 (pt0) REVERT: C 111 LYS cc_start: 0.1785 (pttt) cc_final: 0.1118 (pptt) REVERT: C 129 ILE cc_start: 0.9072 (mt) cc_final: 0.8826 (mt) REVERT: C 133 ASN cc_start: 0.7521 (m-40) cc_final: 0.7160 (m110) outliers start: 8 outliers final: 6 residues processed: 117 average time/residue: 0.1211 time to fit residues: 19.2745 Evaluate side-chains 99 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4791 r_free = 0.4791 target = 0.162089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.147968 restraints weight = 45236.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.152107 restraints weight = 22746.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.154768 restraints weight = 13673.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.156555 restraints weight = 9038.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.157915 restraints weight = 6386.285| |-----------------------------------------------------------------------------| r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4891 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= 0.140 Angle : 0.552 6.439 6510 Z= 0.294 Chirality : 0.036 0.121 834 Planarity : 0.003 0.027 792 Dihedral : 3.445 14.978 630 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.10 % Allowed : 19.77 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.35), residues: 606 helix: 2.06 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -4.01 (0.36), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 77 PHE 0.016 0.001 PHE C 117 HIS 0.006 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4782) covalent geometry : angle 0.55209 ( 6510) hydrogen bonds : bond 0.03888 ( 366) hydrogen bonds : angle 3.61880 ( 1098) *********************** 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 111 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.265 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: B 129 ILE cc_start: 0.9036 (mt) cc_final: 0.8713 (mt) REVERT: C 111 LYS cc_start: 0.1858 (pttt) cc_final: 0.1434 (pptt) REVERT: C 129 ILE cc_start: 0.9177 (mt) cc_final: 0.8735 (mt) REVERT: C 133 ASN cc_start: 0.7855 (m-40) cc_final: 0.7429 (m110) outliers start: 16 outliers final: 11 residues processed: 108 average time/residue: 0.1111 time to fit residues: 16.6225 Evaluate side-chains 99 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 104 TYR 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 104 TYR 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 104 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.154690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.137296 restraints weight = 44436.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.142895 restraints weight = 19461.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.146311 restraints weight = 10638.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.148491 restraints weight = 6654.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.149761 restraints weight = 4475.066| |-----------------------------------------------------------------------------| r_work (final): 0.4708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4782 Z= 0.116 Angle : 0.524 5.222 6510 Z= 0.279 Chirality : 0.036 0.127 834 Planarity : 0.003 0.027 792 Dihedral : 3.290 14.045 630 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.33 % Allowed : 20.35 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.35), residues: 606 helix: 2.26 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -4.08 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.000 TYR E 104 PHE 0.018 0.001 PHE B 117 HIS 0.008 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4782) covalent geometry : angle 0.52357 ( 6510) hydrogen bonds : bond 0.03687 ( 366) hydrogen bonds : angle 3.45088 ( 1098) *********************** 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 104 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.198 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: symmetry clash revert: symmetry clash REVERT: D 49 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9010 (mm-30) REVERT: B 70 GLN cc_start: 0.8452 (mt0) cc_final: 0.8032 (pt0) REVERT: C 111 LYS cc_start: 0.1844 (pttt) cc_final: 0.1419 (pptt) REVERT: C 129 ILE cc_start: 0.8897 (mt) cc_final: 0.8556 (mt) REVERT: C 133 ASN cc_start: 0.8170 (m-40) cc_final: 0.7662 (m110) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 0.1050 time to fit residues: 14.8418 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 : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 104 TYR 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 104 TYR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.164458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.149371 restraints weight = 36286.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.154539 restraints weight = 14391.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.157739 restraints weight = 7213.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.159695 restraints weight = 4068.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.160893 restraints weight = 2512.170| |-----------------------------------------------------------------------------| r_work (final): 0.4803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.5550 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= 0.102 Angle : 0.512 6.880 6510 Z= 0.268 Chirality : 0.036 0.134 834 Planarity : 0.003 0.028 792 Dihedral : 3.217 14.216 630 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.13 % Allowed : 18.99 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.36), residues: 606 helix: 2.50 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -4.14 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.000 TYR E 104 PHE 0.020 0.001 PHE A 117 HIS 0.005 0.000 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4782) covalent geometry : angle 0.51167 ( 6510) hydrogen bonds : bond 0.03387 ( 366) hydrogen bonds : angle 3.28336 ( 1098) *********************** 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 109 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.208 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: symmetry clash revert: symmetry clash REVERT: D 49 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8991 (mm-30) REVERT: A 129 ILE cc_start: 0.8761 (mt) cc_final: 0.8544 (mt) REVERT: A 133 ASN cc_start: 0.7858 (m-40) cc_final: 0.7481 (m110) REVERT: B 70 GLN cc_start: 0.8287 (mt0) cc_final: 0.7750 (pt0) REVERT: C 111 LYS cc_start: 0.2008 (pttt) cc_final: 0.1544 (pptt) REVERT: C 129 ILE cc_start: 0.8908 (mt) cc_final: 0.8660 (mt) REVERT: C 133 ASN cc_start: 0.8125 (m-40) cc_final: 0.7645 (m110) outliers start: 11 outliers final: 9 residues processed: 108 average time/residue: 0.1171 time to fit residues: 17.6851 Evaluate side-chains 101 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 104 TYR Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4678 r_free = 0.4678 target = 0.156149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.138313 restraints weight = 45054.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.144148 restraints weight = 19543.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.147703 restraints weight = 10516.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.149983 restraints weight = 6540.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.151515 restraints weight = 4366.775| |-----------------------------------------------------------------------------| r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.5825 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= 0.103 Angle : 0.510 6.785 6510 Z= 0.270 Chirality : 0.036 0.135 834 Planarity : 0.003 0.027 792 Dihedral : 3.133 13.337 630 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.33 % Allowed : 18.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.36), residues: 606 helix: 2.50 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -4.16 (0.35), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.000 TYR E 77 PHE 0.017 0.001 PHE E 76 HIS 0.005 0.000 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 4782) covalent geometry : angle 0.50954 ( 6510) hydrogen bonds : bond 0.03312 ( 366) hydrogen bonds : angle 3.26946 ( 1098) *********************** 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 107 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.297 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: 0.9280 (mm-30) cc_final: 0.9050 (mm-30) REVERT: B 70 GLN cc_start: 0.8460 (mt0) cc_final: 0.7854 (pt0) REVERT: C 111 LYS cc_start: 0.1933 (pttt) cc_final: 0.1522 (pptt) REVERT: C 129 ILE cc_start: 0.8840 (mt) cc_final: 0.8582 (mt) REVERT: C 133 ASN cc_start: 0.8146 (m-40) cc_final: 0.7646 (m110) outliers start: 12 outliers final: 11 residues processed: 104 average time/residue: 0.1208 time to fit residues: 17.5389 Evaluate side-chains 102 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 104 TYR Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.4708 r_free = 0.4708 target = 0.160313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.145699 restraints weight = 36311.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.150574 restraints weight = 13957.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.153605 restraints weight = 7046.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.155450 restraints weight = 3998.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.156594 restraints weight = 2480.373| |-----------------------------------------------------------------------------| r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4782 Z= 0.148 Angle : 0.556 6.503 6510 Z= 0.303 Chirality : 0.037 0.139 834 Planarity : 0.003 0.026 792 Dihedral : 3.389 13.599 630 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.91 % Allowed : 19.77 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.35), residues: 606 helix: 1.91 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -4.06 (0.37), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR F 104 PHE 0.017 0.002 PHE B 135 HIS 0.006 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4782) covalent geometry : angle 0.55559 ( 6510) hydrogen bonds : bond 0.03840 ( 366) hydrogen bonds : angle 3.61787 ( 1098) *********************** 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 106 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.280 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: symmetry clash REVERT: D 49 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8965 (mm-30) REVERT: B 70 GLN cc_start: 0.8154 (mt0) cc_final: 0.7540 (pt0) REVERT: C 111 LYS cc_start: 0.2274 (pttt) cc_final: 0.2063 (pttt) REVERT: C 129 ILE cc_start: 0.9070 (mt) cc_final: 0.8725 (mt) REVERT: C 133 ASN cc_start: 0.8180 (m-40) cc_final: 0.7623 (m110) outliers start: 15 outliers final: 14 residues processed: 104 average time/residue: 0.1215 time to fit residues: 17.4435 Evaluate side-chains 100 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 104 TYR 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 139 PHE Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.152141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.135385 restraints weight = 43862.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.140831 restraints weight = 18608.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.144328 restraints weight = 10129.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.146495 restraints weight = 6118.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.147956 restraints weight = 4018.666| |-----------------------------------------------------------------------------| r_work (final): 0.4791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.6527 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= 0.117 Angle : 0.528 6.627 6510 Z= 0.284 Chirality : 0.037 0.156 834 Planarity : 0.003 0.025 792 Dihedral : 3.300 13.346 630 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.13 % Allowed : 20.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.35), residues: 606 helix: 2.06 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -4.12 (0.36), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 77 PHE 0.012 0.001 PHE A 135 HIS 0.005 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4782) covalent geometry : angle 0.52845 ( 6510) hydrogen bonds : bond 0.03495 ( 366) hydrogen bonds : angle 3.43780 ( 1098) *********************** 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 101 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.199 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: 0.8517 (mt0) cc_final: 0.7901 (pt0) REVERT: C 129 ILE cc_start: 0.8856 (mt) cc_final: 0.8601 (mt) REVERT: C 133 ASN cc_start: 0.8241 (m-40) cc_final: 0.7682 (m110) outliers start: 11 outliers final: 9 residues processed: 99 average time/residue: 0.1127 time to fit residues: 15.7338 Evaluate side-chains 97 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 104 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.164648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.149466 restraints weight = 35934.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.154994 restraints weight = 13518.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.158353 restraints weight = 6538.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.160318 restraints weight = 3453.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.161430 restraints weight = 1994.974| |-----------------------------------------------------------------------------| r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.6675 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= 0.104 Angle : 0.528 6.718 6510 Z= 0.280 Chirality : 0.037 0.157 834 Planarity : 0.003 0.027 792 Dihedral : 3.177 13.398 630 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.94 % Allowed : 20.74 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.36), residues: 606 helix: 2.22 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -4.20 (0.35), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR A 77 PHE 0.022 0.001 PHE A 117 HIS 0.005 0.000 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 4782) covalent geometry : angle 0.52774 ( 6510) hydrogen bonds : bond 0.03277 ( 366) hydrogen bonds : angle 3.31682 ( 1098) ********************** 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 108 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.262 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: symmetry clash REVERT: A 70 GLN cc_start: 0.7805 (mt0) cc_final: 0.7274 (pt0) REVERT: B 70 GLN cc_start: 0.8091 (mt0) cc_final: 0.7533 (pt0) REVERT: C 129 ILE cc_start: 0.9065 (mt) cc_final: 0.8719 (mt) REVERT: C 133 ASN cc_start: 0.8176 (m-40) cc_final: 0.7609 (m110) outliers start: 10 outliers final: 9 residues processed: 105 average time/residue: 0.1149 time to fit residues: 16.7596 Evaluate side-chains 101 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 104 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.166180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.151893 restraints weight = 36156.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.156785 restraints weight = 13190.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.159876 restraints weight = 6241.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.161609 restraints weight = 3213.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.162630 restraints weight = 1819.569| |-----------------------------------------------------------------------------| r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.6827 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= 0.102 Angle : 0.517 6.909 6510 Z= 0.275 Chirality : 0.036 0.151 834 Planarity : 0.003 0.026 792 Dihedral : 3.106 12.470 630 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.33 % Allowed : 20.54 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.36), residues: 606 helix: 2.33 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -4.21 (0.35), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR A 77 PHE 0.014 0.001 PHE A 117 HIS 0.005 0.000 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 4782) covalent geometry : angle 0.51749 ( 6510) hydrogen bonds : bond 0.03177 ( 366) hydrogen bonds : angle 3.27500 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1661.42 seconds wall clock time: 28 minutes 56.41 seconds (1736.41 seconds total)