Starting phenix.real_space_refine on Thu Oct 22 22:07:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28no_56657/10_2026/28no_56657.cif Found real_map, /net/cci-nas-00/data/ceres_data/28no_56657/10_2026/28no_56657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28no_56657/10_2026/28no_56657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28no_56657/10_2026/28no_56657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28no_56657/10_2026/28no_56657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28no_56657/10_2026/28no_56657.map" } resolution = 4.1 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians K 1 8.98 5 S 19 5.16 5 C 2044 2.51 5 N 477 2.21 5 O 543 1.98 5 H 3141 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6225 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 576 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1412 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1412 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "C" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1412 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "D" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1412 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.94, per 1000 atoms: 0.15 Number of scatterers: 6225 At special positions: 0 Unit cell: (67.15, 65.45, 87.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 1 19.00 S 19 16.00 O 543 8.00 N 477 7.00 C 2044 6.00 H 3141 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 28 " distance=2.03 Simple disulfide: pdb=" SG CYS E 13 " - pdb=" SG CYS E 33 " distance=2.03 Simple disulfide: pdb=" SG CYS E 17 " - pdb=" SG CYS E 35 " distance=2.03 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 111.9 milliseconds 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 712 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'E' and resid 9 through 17 removed outlier: 4.252A pdb=" N CYS E 13 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N CYS E 17 " --> pdb=" O CYS E 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 43 removed outlier: 4.398A pdb=" N LEU A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 69 through 106 removed outlier: 3.544A pdb=" N MET A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 43 removed outlier: 4.101A pdb=" N LEU B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY B 43 " --> pdb=" O HIS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.710A pdb=" N TYR B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 108 removed outlier: 3.824A pdb=" N PHE B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 41 removed outlier: 4.281A pdb=" N LEU C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.816A pdb=" N TYR C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 105 removed outlier: 4.324A pdb=" N PHE C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 42 removed outlier: 3.578A pdb=" N ALA D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE D 32 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'D' and resid 69 through 105 removed outlier: 3.781A pdb=" N MET D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR D 74 " --> pdb=" O PRO D 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE D 97 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 639 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: 1.13 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 3141 1.02 - 1.22: 1 1.22 - 1.42: 1326 1.42 - 1.62: 1797 1.62 - 1.81: 32 Bond restraints: 6297 Sorted by residual: bond pdb=" CA PCA E 1 " pdb=" CB PCA E 1 " ideal model delta sigma weight residual 1.530 1.510 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" OG1 THR C 59 " pdb=" HG1 THR C 59 " ideal model delta sigma weight residual 0.840 0.825 0.015 2.00e-02 2.50e+03 5.82e-01 bond pdb=" OG1 THR B 59 " pdb=" HG1 THR B 59 " ideal model delta sigma weight residual 0.840 0.825 0.015 2.00e-02 2.50e+03 5.51e-01 bond pdb=" N LEU B 82 " pdb=" CA LEU B 82 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.28e-02 6.10e+03 5.16e-01 bond pdb=" C PCA E 1 " pdb=" O PCA E 1 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 5.13e-01 ... (remaining 6292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 10794 1.37 - 2.73: 537 2.73 - 4.10: 25 4.10 - 5.46: 4 5.46 - 6.83: 3 Bond angle restraints: 11363 Sorted by residual: angle pdb=" O PCA E 1 " pdb=" C PCA E 1 " pdb=" N PHE E 2 " ideal model delta sigma weight residual 123.00 129.83 -6.83 1.60e+00 3.91e-01 1.82e+01 angle pdb=" CA PCA E 1 " pdb=" C PCA E 1 " pdb=" O PCA E 1 " ideal model delta sigma weight residual 120.80 113.98 6.82 1.70e+00 3.46e-01 1.61e+01 angle pdb=" C VAL A 91 " pdb=" N GLU A 92 " pdb=" CA GLU A 92 " ideal model delta sigma weight residual 120.29 116.88 3.41 1.42e+00 4.96e-01 5.76e+00 angle pdb=" C VAL D 91 " pdb=" N GLU D 92 " pdb=" CA GLU D 92 " ideal model delta sigma weight residual 120.31 116.91 3.40 1.52e+00 4.33e-01 5.01e+00 angle pdb=" CA PCA E 1 " pdb=" N PCA E 1 " pdb=" CD PCA E 1 " ideal model delta sigma weight residual 114.17 108.42 5.75 3.00e+00 1.11e-01 3.67e+00 ... (remaining 11358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 2638 14.51 - 29.03: 158 29.03 - 43.54: 53 43.54 - 58.05: 69 58.05 - 72.57: 42 Dihedral angle restraints: 2960 sinusoidal: 1561 harmonic: 1399 Sorted by residual: dihedral pdb=" CA CYS E 7 " pdb=" C CYS E 7 " pdb=" N THR E 8 " pdb=" CA THR E 8 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA MET E 29 " pdb=" C MET E 29 " pdb=" N ASN E 30 " pdb=" CA ASN E 30 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU A 25 " pdb=" C LEU A 25 " pdb=" N LEU A 26 " pdb=" CA LEU A 26 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 2957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 291 0.030 - 0.061: 185 0.061 - 0.091: 29 0.091 - 0.122: 13 0.122 - 0.152: 1 Chirality restraints: 519 Sorted by residual: chirality pdb=" CA PRO B 70 " pdb=" N PRO B 70 " pdb=" C PRO B 70 " pdb=" CB PRO B 70 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA THR B 59 " pdb=" N THR B 59 " pdb=" C THR B 59 " pdb=" CB THR B 59 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA VAL E 5 " pdb=" N VAL E 5 " pdb=" C VAL E 5 " pdb=" CB VAL E 5 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 516 not shown) Planarity restraints: 890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 29 " 0.029 2.00e-02 2.50e+03 5.65e-02 3.20e+01 pdb=" N ASN E 30 " -0.097 2.00e-02 2.50e+03 pdb=" CA ASN E 30 " 0.025 2.00e-02 2.50e+03 pdb=" H ASN E 30 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 39 " 0.004 2.00e-02 2.50e+03 2.53e-02 1.44e+01 pdb=" CG HIS C 39 " -0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS C 39 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS C 39 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS C 39 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS C 39 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS C 39 " 0.046 2.00e-02 2.50e+03 pdb=" HD2 HIS C 39 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 HIS C 39 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 28 " 0.018 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" N ALA C 29 " -0.059 2.00e-02 2.50e+03 pdb=" CA ALA C 29 " 0.015 2.00e-02 2.50e+03 pdb=" H ALA C 29 " 0.026 2.00e-02 2.50e+03 ... (remaining 887 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.53: 4584 2.53 - 3.18: 17461 3.18 - 3.83: 20638 3.83 - 4.49: 30540 4.49 - 5.14: 45613 Nonbonded interactions: 118836 Sorted by model distance: nonbonded pdb=" H THR D 76 " pdb=" HG1 THR D 76 " model vdw 1.875 2.100 nonbonded pdb=" O ALA B 58 " pdb=" HG1 THR B 59 " model vdw 1.889 2.450 nonbonded pdb=" O ALA A 58 " pdb=" HG1 THR A 59 " model vdw 1.896 2.450 nonbonded pdb=" O ALA C 58 " pdb=" HG1 THR C 59 " model vdw 1.897 2.450 nonbonded pdb=" O ALA D 58 " pdb=" HG1 THR D 59 " model vdw 1.897 2.450 ... (remaining 118831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 108) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.110 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.980 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.003 0.023 3159 Z= 0.155 Angle : 0.641 6.828 4303 Z= 0.395 Chirality : 0.039 0.152 519 Planarity : 0.007 0.041 510 Dihedral : 12.556 72.566 1073 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.30 % Allowed : 3.02 % Favored : 96.68 % 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 are not related in a simple way. whole: -2.44 (0.39), residues: 382 helix: -1.93 (0.24), residues: 298 sheet: None (None), residues: 0 loop : 0.67 (0.81), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG D 93 TYR 0.036 0.005 TYR D 74 PHE 0.009 0.002 PHE C 40 TRP 0.021 0.005 TRP D 52 HIS 0.006 0.002 HIS B 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 ( 3156) covalent geometry : angle 0.64132 / 0.40 ( 4297) SS BOND : bond 0.00255 / 0.13 ( 3) SS BOND : angle 0.66049 / 0.24 ( 6) hydrogen bonds : bond 0.09613 / 6.23 ( 213) hydrogen bonds : angle 5.72402 / 3.82 ( 639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 LYS cc_start: 0.8409 (tttt) cc_final: 0.8112 (tppt) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1311 time to fit residues: 11.2608 Evaluate side-chains 49 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 13] chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.154381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140808 restraints weight = 13025.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.144612 restraints weight = 8185.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.146054 restraints weight = 5805.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.147418 restraints weight = 4525.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.148660 restraints weight = 3644.004| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3159 Z= 0.145 Angle : 0.533 4.212 4303 Z= 0.297 Chirality : 0.037 0.118 519 Planarity : 0.003 0.030 510 Dihedral : 5.043 28.679 427 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.43), residues: 382 helix: -0.43 (0.28), residues: 307 sheet: None (None), residues: 0 loop : 0.35 (0.86), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.009 0.001 TYR A 51 PHE 0.015 0.001 PHE A 54 TRP 0.008 0.001 TRP C 52 HIS 0.004 0.002 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3156) covalent geometry : angle 0.53243 / 0.30 ( 4297) SS BOND : bond 0.00598 / 0.31 ( 3) SS BOND : angle 0.73497 / 0.29 ( 6) hydrogen bonds : bond 0.05258 / 3.53 ( 213) hydrogen bonds : angle 4.33930 / 2.89 ( 639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 62 TYR cc_start: 0.8964 (m-80) cc_final: 0.8745 (m-80) REVERT: A 73 MET cc_start: 0.7952 (mtt) cc_final: 0.7750 (mtt) REVERT: B 41 ILE cc_start: 0.8538 (mt) cc_final: 0.8224 (mt) REVERT: B 93 ARG cc_start: 0.7196 (tpt-90) cc_final: 0.6791 (tmm160) REVERT: C 73 MET cc_start: 0.6117 (mtp) cc_final: 0.5195 (mmt) REVERT: D 73 MET cc_start: 0.8259 (mtm) cc_final: 0.8018 (mtp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1233 time to fit residues: 9.4623 Evaluate side-chains 48 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [30, 12, 28, 10, 13, 25, 22, 27, 16, 24, 8] chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.150869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137875 restraints weight = 12812.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.141497 restraints weight = 8269.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.143162 restraints weight = 5833.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.144973 restraints weight = 4381.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.146315 restraints weight = 3365.677| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3159 Z= 0.136 Angle : 0.494 4.320 4303 Z= 0.275 Chirality : 0.036 0.114 519 Planarity : 0.003 0.037 510 Dihedral : 4.677 30.311 427 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.44), residues: 382 helix: 0.20 (0.30), residues: 303 sheet: None (None), residues: 0 loop : 0.28 (0.85), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.007 0.001 TYR A 51 PHE 0.020 0.001 PHE B 54 TRP 0.008 0.001 TRP C 52 HIS 0.004 0.002 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 3156) covalent geometry : angle 0.49350 / 0.27 ( 4297) SS BOND : bond 0.00388 / 0.19 ( 3) SS BOND : angle 0.88531 / 0.36 ( 6) hydrogen bonds : bond 0.05080 / 3.37 ( 213) hydrogen bonds : angle 4.08644 / 2.73 ( 639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ILE cc_start: 0.8568 (mt) cc_final: 0.8261 (mt) REVERT: D 73 MET cc_start: 0.8225 (mtm) cc_final: 0.8017 (mtt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1242 time to fit residues: 8.8989 Evaluate side-chains 47 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [21, 7, 30, 4, 24, 3, 6, 10, 26, 16, 13] chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.0470 chunk 6 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.159615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.146965 restraints weight = 12448.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.150242 restraints weight = 7950.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.152134 restraints weight = 5525.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.153051 restraints weight = 4134.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.154802 restraints weight = 3441.070| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3159 Z= 0.118 Angle : 0.464 4.727 4303 Z= 0.254 Chirality : 0.035 0.129 519 Planarity : 0.002 0.015 510 Dihedral : 4.390 34.170 427 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.44), residues: 382 helix: 0.68 (0.30), residues: 303 sheet: None (None), residues: 0 loop : 0.10 (0.83), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 19 TYR 0.007 0.001 TYR A 51 PHE 0.008 0.001 PHE E 2 TRP 0.006 0.001 TRP C 52 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 3156) covalent geometry : angle 0.46334 / 0.25 ( 4297) SS BOND : bond 0.00300 / 0.15 ( 3) SS BOND : angle 0.89970 / 0.33 ( 6) hydrogen bonds : bond 0.04755 / 3.16 ( 213) hydrogen bonds : angle 3.82305 / 2.54 ( 639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8083 (mmp) cc_final: 0.7610 (tpp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1139 time to fit residues: 8.3828 Evaluate side-chains 50 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [12, 23, 1, 4, 7, 24, 14, 31, 5, 25, 0] chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.184770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.174106 restraints weight = 11118.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.177492 restraints weight = 6629.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.179149 restraints weight = 4328.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.181071 restraints weight = 3172.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.181325 restraints weight = 2290.304| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3159 Z= 0.127 Angle : 0.498 6.976 4303 Z= 0.271 Chirality : 0.035 0.121 519 Planarity : 0.002 0.021 510 Dihedral : 4.702 42.095 427 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: 1.10 (0.45), residues: 382 helix: 0.98 (0.30), residues: 303 sheet: None (None), residues: 0 loop : 0.12 (0.86), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.007 0.001 TYR A 51 PHE 0.017 0.001 PHE D 54 TRP 0.005 0.001 TRP C 52 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 3156) covalent geometry : angle 0.48957 / 0.27 ( 4297) SS BOND : bond 0.00925 / 0.48 ( 3) SS BOND : angle 2.48075 / 1.06 ( 6) hydrogen bonds : bond 0.04767 / 3.17 ( 213) hydrogen bonds : angle 3.80833 / 2.52 ( 639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7734 (tpp-160) cc_final: 0.7525 (tpp-160) REVERT: C 104 MET cc_start: 0.8077 (mmp) cc_final: 0.7619 (tpp) REVERT: D 42 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7006 (mm-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1342 time to fit residues: 9.1946 Evaluate side-chains 49 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [6, 31, 15, 19, 22, 33, 16, 10, 26, 29, 21] chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.170394 restraints weight = 11028.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.173709 restraints weight = 6499.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175405 restraints weight = 4260.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177171 restraints weight = 3081.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.177796 restraints weight = 2353.810| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3159 Z= 0.135 Angle : 0.489 5.019 4303 Z= 0.272 Chirality : 0.035 0.124 519 Planarity : 0.003 0.027 510 Dihedral : 4.656 39.866 427 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: 1.32 (0.45), residues: 382 helix: 1.17 (0.30), residues: 303 sheet: None (None), residues: 0 loop : 0.02 (0.85), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.008 0.001 TYR A 51 PHE 0.007 0.001 PHE A 75 TRP 0.005 0.001 TRP C 52 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 3156) covalent geometry : angle 0.48474 / 0.27 ( 4297) SS BOND : bond 0.00628 / 0.32 ( 3) SS BOND : angle 1.85395 / 0.77 ( 6) hydrogen bonds : bond 0.04970 / 3.30 ( 213) hydrogen bonds : angle 3.82186 / 2.53 ( 639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7660 (tp-100) REVERT: C 104 MET cc_start: 0.8169 (mmp) cc_final: 0.7663 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1406 time to fit residues: 8.8823 Evaluate side-chains 46 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [5, 31, 3, 4, 28, 18, 9, 1, 2, 23, 0] chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.181213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170459 restraints weight = 11001.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173859 restraints weight = 6418.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.175487 restraints weight = 4169.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177061 restraints weight = 3004.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.177682 restraints weight = 2307.215| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3159 Z= 0.128 Angle : 0.475 4.823 4303 Z= 0.262 Chirality : 0.035 0.120 519 Planarity : 0.003 0.029 510 Dihedral : 4.544 40.385 427 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: 1.58 (0.45), residues: 382 helix: 1.37 (0.30), residues: 303 sheet: None (None), residues: 0 loop : 0.03 (0.85), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.006 0.001 TYR A 51 PHE 0.008 0.001 PHE D 54 TRP 0.005 0.001 TRP C 52 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 3156) covalent geometry : angle 0.47144 / 0.26 ( 4297) SS BOND : bond 0.00552 / 0.28 ( 3) SS BOND : angle 1.54207 / 0.66 ( 6) hydrogen bonds : bond 0.04891 / 3.26 ( 213) hydrogen bonds : angle 3.77354 / 2.50 ( 639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7783 (tp-100) REVERT: C 104 MET cc_start: 0.7943 (mmp) cc_final: 0.7572 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1378 time to fit residues: 8.4192 Evaluate side-chains 43 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [25, 29, 2, 33, 26, 14, 23, 11, 12, 8, 7] chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.155742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142843 restraints weight = 12302.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.145940 restraints weight = 7885.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147884 restraints weight = 5529.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.149506 restraints weight = 4140.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150448 restraints weight = 3306.163| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3159 Z= 0.136 Angle : 0.489 5.028 4303 Z= 0.272 Chirality : 0.035 0.120 519 Planarity : 0.003 0.030 510 Dihedral : 4.605 43.256 427 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: 1.64 (0.45), residues: 382 helix: 1.44 (0.30), residues: 303 sheet: None (None), residues: 0 loop : -0.05 (0.85), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.008 0.001 TYR A 51 PHE 0.010 0.001 PHE C 54 TRP 0.003 0.001 TRP C 52 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 3156) covalent geometry : angle 0.48692 / 0.27 ( 4297) SS BOND : bond 0.00550 / 0.28 ( 3) SS BOND : angle 1.39078 / 0.59 ( 6) hydrogen bonds : bond 0.05037 / 3.37 ( 213) hydrogen bonds : angle 3.82360 / 2.53 ( 639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8005 (mmp) cc_final: 0.7599 (tpp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1510 time to fit residues: 8.9880 Evaluate side-chains 42 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [23, 6, 0, 8, 18, 27, 24, 34, 32, 4, 9] chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145808 restraints weight = 12251.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149497 restraints weight = 7559.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150887 restraints weight = 5090.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152334 restraints weight = 3840.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.153599 restraints weight = 2979.014| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3159 Z= 0.128 Angle : 0.476 5.388 4303 Z= 0.263 Chirality : 0.035 0.119 519 Planarity : 0.003 0.031 510 Dihedral : 4.521 42.496 427 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: 1.73 (0.46), residues: 382 helix: 1.51 (0.30), residues: 303 sheet: None (None), residues: 0 loop : -0.05 (0.85), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 19 TYR 0.005 0.001 TYR A 65 PHE 0.013 0.001 PHE A 54 TRP 0.005 0.001 TRP A 46 HIS 0.002 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 3156) covalent geometry : angle 0.47370 / 0.26 ( 4297) SS BOND : bond 0.00487 / 0.25 ( 3) SS BOND : angle 1.33453 / 0.57 ( 6) hydrogen bonds : bond 0.04854 / 3.26 ( 213) hydrogen bonds : angle 3.74823 / 2.47 ( 639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.7999 (mmp) cc_final: 0.7594 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1404 time to fit residues: 8.6168 Evaluate side-chains 43 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [8, 4, 0, 5, 33, 12, 32, 19, 25, 30, 6] chunk 8 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142499 restraints weight = 12350.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.145818 restraints weight = 7849.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147654 restraints weight = 5454.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.148947 restraints weight = 4075.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.150210 restraints weight = 3251.071| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3159 Z= 0.144 Angle : 0.495 4.533 4303 Z= 0.278 Chirality : 0.036 0.117 519 Planarity : 0.003 0.031 510 Dihedral : 4.651 45.689 427 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.45), residues: 382 helix: 1.43 (0.30), residues: 303 sheet: None (None), residues: 0 loop : -0.17 (0.84), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.006 0.001 TYR C 33 PHE 0.009 0.001 PHE A 54 TRP 0.004 0.001 TRP C 46 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 3156) covalent geometry : angle 0.49239 / 0.28 ( 4297) SS BOND : bond 0.00575 / 0.29 ( 3) SS BOND : angle 1.33497 / 0.56 ( 6) hydrogen bonds : bond 0.05142 / 3.45 ( 213) hydrogen bonds : angle 3.86181 / 2.55 ( 639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.7983 (mmp) cc_final: 0.7565 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1256 time to fit residues: 8.0114 Evaluate side-chains 44 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [24, 17, 20, 27, 1, 25, 10, 22, 19, 8, 6] chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.0000 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.0170 chunk 8 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 overall best weight: 0.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.157748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145223 restraints weight = 12598.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.148395 restraints weight = 7997.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150640 restraints weight = 5536.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.152220 restraints weight = 4054.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.153076 restraints weight = 3163.433| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3159 Z= 0.104 Angle : 0.445 5.334 4303 Z= 0.244 Chirality : 0.034 0.118 519 Planarity : 0.002 0.033 510 Dihedral : 4.255 38.917 427 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.46), residues: 382 helix: 1.82 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -0.11 (0.84), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 19 TYR 0.005 0.001 TYR A 65 PHE 0.012 0.001 PHE A 54 TRP 0.005 0.001 TRP C 52 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 3156) covalent geometry : angle 0.44273 / 0.24 ( 4297) SS BOND : bond 0.00377 / 0.19 ( 3) SS BOND : angle 1.29523 / 0.57 ( 6) hydrogen bonds : bond 0.04475 / 3.01 ( 213) hydrogen bonds : angle 3.58582 / 2.37 ( 639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.22 seconds wall clock time: 24 minutes 29.51 seconds (1469.51 seconds total)