Starting phenix.real_space_refine on Thu Jul 2 00:43:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wb4_65833/07_2026/9wb4_65833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wb4_65833/07_2026/9wb4_65833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wb4_65833/07_2026/9wb4_65833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wb4_65833/07_2026/9wb4_65833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wb4_65833/07_2026/9wb4_65833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wb4_65833/07_2026/9wb4_65833.map" } resolution = 3.32 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= 0.011 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 P 75 5.49 5 S 15 5.16 5 C 2678 2.51 5 N 812 2.21 5 O 1142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4722 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1382 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "C" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "R" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.92, per 1000 atoms: 0.19 Number of scatterers: 4722 At special positions: 0 Unit cell: (88.32, 73.92, 132.48, 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 15 16.00 P 75 15.00 O 1142 8.00 N 812 7.00 C 2678 6.00 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: 0.28 Conformation dependent library (CDL) restraints added in 80.9 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 47.7% beta 25 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.685A pdb=" N ILE A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.775A pdb=" N GLN A 145 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.558A pdb=" N TYR A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 178 " --> pdb=" O LYS A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.622A pdb=" N SER B 33 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 34 " --> pdb=" O PHE B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 34' Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.643A pdb=" N ASP C 29 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.798A pdb=" N ASP C 81 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.519A pdb=" N LEU A 28 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 72 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 58 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP A 78 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 56 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 126 removed outlier: 6.980A pdb=" N MET A 120 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 135 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A 122 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 133 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ARG A 133 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALA A 171 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS A 160 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 150 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 99 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 115 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 105 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 10 Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.098A pdb=" N ARG B 40 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14 removed outlier: 4.339A pdb=" N VAL B 117 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.596A pdb=" N THR C 104 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.848A pdb=" N TRP C 34 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 94 " --> pdb=" O ASP C 91 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 0.51 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1206 1.33 - 1.45: 1328 1.45 - 1.57: 2262 1.57 - 1.69: 148 1.69 - 1.81: 22 Bond restraints: 4966 Sorted by residual: bond pdb=" CA ARG A 84 " pdb=" C ARG A 84 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.24e-02 6.50e+03 1.17e+01 bond pdb=" P A R 13 " pdb=" OP2 A R 13 " ideal model delta sigma weight residual 1.485 1.527 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" P G R 12 " pdb=" OP2 G R 12 " ideal model delta sigma weight residual 1.485 1.526 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C ARG A 84 " pdb=" N ASP A 85 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.44e-02 4.82e+03 4.08e+00 bond pdb=" N VAL C 105 " pdb=" CA VAL C 105 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.04e+00 ... (remaining 4961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6705 1.71 - 3.41: 322 3.41 - 5.12: 36 5.12 - 6.83: 14 6.83 - 8.54: 2 Bond angle restraints: 7079 Sorted by residual: angle pdb=" CA THR C 104 " pdb=" C THR C 104 " pdb=" O THR C 104 " ideal model delta sigma weight residual 120.36 124.63 -4.27 1.08e+00 8.57e-01 1.56e+01 angle pdb=" C1' C R 57 " pdb=" N1 C R 57 " pdb=" C2 C R 57 " ideal model delta sigma weight residual 118.80 122.61 -3.81 1.10e+00 8.26e-01 1.20e+01 angle pdb=" O3' A R 4 " pdb=" P A R 5 " pdb=" O5' A R 5 " ideal model delta sigma weight residual 104.00 98.81 5.19 1.50e+00 4.44e-01 1.20e+01 angle pdb=" O3' U R 14 " pdb=" C3' U R 14 " pdb=" C2' U R 14 " ideal model delta sigma weight residual 113.70 118.12 -4.42 1.50e+00 4.44e-01 8.69e+00 angle pdb=" C3' U R 14 " pdb=" O3' U R 14 " pdb=" P G R 15 " ideal model delta sigma weight residual 120.20 124.29 -4.09 1.50e+00 4.44e-01 7.43e+00 ... (remaining 7074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.95: 2660 22.95 - 45.90: 236 45.90 - 68.84: 139 68.84 - 91.79: 22 91.79 - 114.74: 1 Dihedral angle restraints: 3058 sinusoidal: 1901 harmonic: 1157 Sorted by residual: dihedral pdb=" O4' A R 59 " pdb=" C1' A R 59 " pdb=" N9 A R 59 " pdb=" C4 A R 59 " ideal model delta sinusoidal sigma weight residual 254.00 178.29 75.71 1 1.70e+01 3.46e-03 2.50e+01 dihedral pdb=" O4' U R 60 " pdb=" C1' U R 60 " pdb=" N1 U R 60 " pdb=" C2 U R 60 " ideal model delta sinusoidal sigma weight residual 232.00 178.74 53.26 1 1.70e+01 3.46e-03 1.33e+01 dihedral pdb=" O4' A R 4 " pdb=" C1' A R 4 " pdb=" N9 A R 4 " pdb=" C4 A R 4 " ideal model delta sinusoidal sigma weight residual -106.00 -154.62 48.62 1 1.70e+01 3.46e-03 1.13e+01 ... (remaining 3055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 689 0.101 - 0.203: 157 0.203 - 0.304: 2 0.304 - 0.406: 4 0.406 - 0.507: 5 Chirality restraints: 857 Sorted by residual: chirality pdb=" P C R 82 " pdb=" OP1 C R 82 " pdb=" OP2 C R 82 " pdb=" O5' C R 82 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" P A R 4 " pdb=" OP1 A R 4 " pdb=" OP2 A R 4 " pdb=" O5' A R 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" P C R 25 " pdb=" OP1 C R 25 " pdb=" OP2 C R 25 " pdb=" O5' C R 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.79e+00 ... (remaining 854 not shown) Planarity restraints: 632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C PHE A 83 " -0.066 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 84 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 7 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO C 8 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 8 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 8 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 71 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C GLU A 71 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU A 71 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.010 2.00e-02 2.50e+03 ... (remaining 629 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 740 2.76 - 3.30: 3870 3.30 - 3.83: 7900 3.83 - 4.37: 9545 4.37 - 4.90: 15180 Nonbonded interactions: 37235 Sorted by model distance: nonbonded pdb=" O2' U R 14 " pdb=" OP1 G R 15 " model vdw 2.227 3.040 nonbonded pdb=" OP2 C R 10 " pdb=" O2' U R 42 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR C 2 " pdb=" O ASP C 25 " model vdw 2.344 3.040 nonbonded pdb=" N6 A R 36 " pdb=" O2 C R 51 " model vdw 2.366 3.120 nonbonded pdb=" NH1 ARG B 69 " pdb=" O SER B 87 " model vdw 2.371 3.120 ... (remaining 37230 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.210 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.900 Find NCS groups from input model: 0.010 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3160 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 : 0.005 0.042 4966 Z= 0.366 Angle : 0.817 8.537 7079 Z= 0.506 Chirality : 0.082 0.507 857 Planarity : 0.005 0.064 632 Dihedral : 20.317 114.738 2328 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % 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 are not related in a simple way. whole: 0.16 (0.43), residues: 405 helix: 1.97 (1.78), residues: 11 sheet: 1.08 (0.40), residues: 182 loop : -0.90 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.011 0.001 TYR B 97 PHE 0.011 0.001 PHE B 70 TRP 0.012 0.001 TRP C 90 HIS 0.002 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.37 ( 4966) covalent geometry : angle 0.81735 / 0.51 ( 7079) hydrogen bonds : bond 0.14654 / 9.14 ( 185) hydrogen bonds : angle 5.01367 / 3.52 ( 435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.120 Fit side-chains REVERT: A 3 ASN cc_start: 0.5758 (m-40) cc_final: 0.5455 (m-40) REVERT: A 13 LYS cc_start: 0.7532 (mttt) cc_final: 0.7309 (mttt) REVERT: B 115 MET cc_start: -0.0195 (mtm) cc_final: -0.0441 (mtm) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0905 time to fit residues: 2.0097 Evaluate side-chains 17 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.0060 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 40.0000 overall best weight: 5.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** 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 = 0.5073 r_free = 0.5073 target = 0.283108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.4646 r_free = 0.4646 target = 0.235771 restraints weight = 9728.696| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 4.67 r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.306 4966 Z= 0.933 Angle : 1.734 24.618 7079 Z= 0.900 Chirality : 0.104 0.554 857 Planarity : 0.011 0.106 632 Dihedral : 22.883 149.481 1622 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.04 % Allowed : 15.45 % Favored : 82.51 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -0.27 (0.41), residues: 405 helix: -0.80 (1.15), residues: 12 sheet: 1.22 (0.40), residues: 172 loop : -1.38 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG A 87 TYR 0.011 0.001 TYR A 60 PHE 0.065 0.008 PHE A 89 TRP 0.013 0.001 TRP C 90 HIS 0.036 0.005 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01826 / 0.93 ( 4966) covalent geometry : angle 1.73352 / 0.90 ( 7079) hydrogen bonds : bond 0.19103 / 11.76 ( 185) hydrogen bonds : angle 5.90702 / 4.16 ( 435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.122 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 20 average time/residue: 0.0858 time to fit residues: 2.2257 Evaluate side-chains 17 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain B residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 50.0000 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.289352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.271815 restraints weight = 10350.868| |-----------------------------------------------------------------------------| r_work (start): 0.4908 rms_B_bonded: 1.61 r_work: 0.4657 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5124 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 4966 Z= 0.350 Angle : 0.908 10.802 7079 Z= 0.499 Chirality : 0.056 0.283 857 Planarity : 0.007 0.085 632 Dihedral : 21.888 129.485 1622 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.46 % Allowed : 17.20 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -0.04 (0.41), residues: 405 helix: 0.81 (1.47), residues: 11 sheet: 1.38 (0.41), residues: 164 loop : -1.22 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 87 TYR 0.010 0.001 TYR A 60 PHE 0.026 0.003 PHE A 83 TRP 0.010 0.001 TRP C 90 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.35 ( 4966) covalent geometry : angle 0.90849 / 0.50 ( 7079) hydrogen bonds : bond 0.10394 / 6.67 ( 185) hydrogen bonds : angle 4.78783 / 3.43 ( 435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.076 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 19 average time/residue: 0.0478 time to fit residues: 1.3460 Evaluate side-chains 17 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 159 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 0.3980 chunk 14 optimal weight: 40.0000 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 0.4980 chunk 33 optimal weight: 50.0000 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 50.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- 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 = 0.5019 r_free = 0.5019 target = 0.277110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.4519 r_free = 0.4519 target = 0.220476 restraints weight = 9612.092| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 6.67 r_work: 0.4230 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.421 4966 Z= 0.745 Angle : 1.438 19.378 7079 Z= 0.763 Chirality : 0.088 0.379 857 Planarity : 0.014 0.293 632 Dihedral : 23.466 127.124 1622 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.37 % Allowed : 13.70 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -0.18 (0.41), residues: 405 helix: -0.42 (1.59), residues: 11 sheet: 1.34 (0.42), residues: 166 loop : -1.32 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 55 TYR 0.012 0.001 TYR A 60 PHE 0.037 0.005 PHE A 83 TRP 0.012 0.001 TRP C 90 HIS 0.011 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01556 / 0.75 ( 4966) covalent geometry : angle 1.43813 / 0.76 ( 7079) hydrogen bonds : bond 0.19407 / 13.02 ( 185) hydrogen bonds : angle 5.61948 / 3.97 ( 435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 14 time to evaluate : 0.091 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 27 average time/residue: 0.0677 time to fit residues: 2.4265 Evaluate side-chains 23 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 40.0000 chunk 2 optimal weight: 0.0970 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 37 optimal weight: 40.0000 chunk 10 optimal weight: 0.0870 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 26 optimal weight: 20.0000 overall best weight: 0.8358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.284125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.247764 restraints weight = 9758.248| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 3.25 r_work: 0.4425 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 4966 Z= 0.235 Angle : 0.721 8.545 7079 Z= 0.436 Chirality : 0.051 0.292 857 Planarity : 0.005 0.062 632 Dihedral : 22.158 109.925 1622 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.46 % Allowed : 16.33 % Favored : 82.22 % 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: 0.04 (0.42), residues: 405 helix: 0.63 (1.48), residues: 11 sheet: 1.26 (0.41), residues: 177 loop : -1.14 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 87 TYR 0.012 0.001 TYR A 60 PHE 0.015 0.002 PHE A 6 TRP 0.008 0.001 TRP C 90 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.24 ( 4966) covalent geometry : angle 0.72134 / 0.44 ( 7079) hydrogen bonds : bond 0.09294 / 6.17 ( 185) hydrogen bonds : angle 4.42061 / 3.22 ( 435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.072 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 18 average time/residue: 0.0432 time to fit residues: 1.1338 Evaluate side-chains 18 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 40.0000 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.5032 r_free = 0.5032 target = 0.281382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.246464 restraints weight = 9841.151| |-----------------------------------------------------------------------------| r_work (start): 0.4673 rms_B_bonded: 3.44 r_work: 0.4332 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.202 4966 Z= 0.352 Angle : 0.857 10.969 7079 Z= 0.490 Chirality : 0.057 0.269 857 Planarity : 0.006 0.089 632 Dihedral : 22.678 108.035 1622 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.92 % Allowed : 14.58 % Favored : 82.51 % 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: 0.21 (0.43), residues: 405 helix: 0.58 (1.52), residues: 11 sheet: 1.33 (0.41), residues: 175 loop : -0.93 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 87 TYR 0.011 0.001 TYR A 60 PHE 0.017 0.002 PHE A 6 TRP 0.009 0.001 TRP C 90 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.35 ( 4966) covalent geometry : angle 0.85652 / 0.49 ( 7079) hydrogen bonds : bond 0.11663 / 7.87 ( 185) hydrogen bonds : angle 4.55158 / 3.31 ( 435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 13 time to evaluate : 0.110 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 23 average time/residue: 0.0787 time to fit residues: 2.3785 Evaluate side-chains 21 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.5024 r_free = 0.5024 target = 0.280682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.238684 restraints weight = 9654.100| |-----------------------------------------------------------------------------| r_work (start): 0.4552 rms_B_bonded: 4.93 r_work (final): 0.4552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.202 4966 Z= 0.382 Angle : 0.907 12.181 7079 Z= 0.510 Chirality : 0.059 0.313 857 Planarity : 0.007 0.097 632 Dihedral : 23.069 139.386 1622 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.92 % Allowed : 14.58 % Favored : 82.51 % 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: 0.24 (0.43), residues: 405 helix: -0.24 (1.43), residues: 11 sheet: 1.31 (0.42), residues: 173 loop : -0.81 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 87 TYR 0.010 0.001 TYR A 60 PHE 0.034 0.003 PHE A 178 TRP 0.010 0.001 TRP C 90 HIS 0.009 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00778 / 0.38 ( 4966) covalent geometry : angle 0.90726 / 0.51 ( 7079) hydrogen bonds : bond 0.12311 / 8.20 ( 185) hydrogen bonds : angle 4.61432 / 3.36 ( 435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 13 time to evaluate : 0.129 Fit side-chains REVERT: B 36 MET cc_start: 0.3339 (mmm) cc_final: 0.3109 (mmm) outliers start: 10 outliers final: 8 residues processed: 21 average time/residue: 0.0636 time to fit residues: 1.9512 Evaluate side-chains 21 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain C residue 80 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 40.0000 chunk 18 optimal weight: 40.0000 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 30.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.5149 r_free = 0.5149 target = 0.329343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.317818 restraints weight = 10834.530| |-----------------------------------------------------------------------------| r_work (start): 0.4942 rms_B_bonded: 0.90 r_work: 0.4677 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4494 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 4966 Z= 0.249 Angle : 0.719 8.549 7079 Z= 0.424 Chirality : 0.050 0.292 857 Planarity : 0.005 0.044 632 Dihedral : 22.675 137.337 1622 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.21 % Allowed : 14.58 % Favored : 82.22 % 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: 0.44 (0.44), residues: 405 helix: 0.45 (1.43), residues: 11 sheet: 1.32 (0.41), residues: 181 loop : -0.65 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 87 TYR 0.013 0.001 TYR A 60 PHE 0.015 0.002 PHE A 6 TRP 0.008 0.001 TRP C 90 HIS 0.007 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.25 ( 4966) covalent geometry : angle 0.71910 / 0.42 ( 7079) hydrogen bonds : bond 0.09600 / 6.48 ( 185) hydrogen bonds : angle 4.29859 / 3.15 ( 435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 14 time to evaluate : 0.126 Fit side-chains REVERT: B 36 MET cc_start: 0.3050 (mmm) cc_final: 0.2744 (mmm) outliers start: 11 outliers final: 8 residues processed: 24 average time/residue: 0.0824 time to fit residues: 2.6267 Evaluate side-chains 22 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain C residue 80 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 50.0000 chunk 30 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 28 optimal weight: 50.0000 chunk 37 optimal weight: 40.0000 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- 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 = 0.4968 r_free = 0.4968 target = 0.272726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.228615 restraints weight = 9019.807| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 5.03 r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.393 4966 Z= 0.923 Angle : 1.684 24.548 7079 Z= 0.862 Chirality : 0.100 0.464 857 Planarity : 0.009 0.057 632 Dihedral : 24.196 139.466 1622 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.17 % Favored : 93.58 % Rotamer: Outliers : 3.50 % Allowed : 13.99 % Favored : 82.51 % Cbeta Deviations : 0.27 % 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: 0.23 (0.43), residues: 405 helix: -1.30 (1.39), residues: 11 sheet: 1.54 (0.43), residues: 163 loop : -0.87 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 87 TYR 0.016 0.001 TYR A 60 PHE 0.049 0.005 PHE A 178 TRP 0.010 0.001 TRP C 90 HIS 0.019 0.003 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01882 / 0.92 ( 4966) covalent geometry : angle 1.68399 / 0.86 ( 7079) hydrogen bonds : bond 0.21474 / 14.39 ( 185) hydrogen bonds : angle 5.62123 / 4.06 ( 435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 12 time to evaluate : 0.127 Fit side-chains REVERT: B 36 MET cc_start: 0.3635 (mmm) cc_final: 0.3274 (mmm) outliers start: 12 outliers final: 10 residues processed: 23 average time/residue: 0.0830 time to fit residues: 2.5479 Evaluate side-chains 22 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 40.0000 chunk 35 optimal weight: 50.0000 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 30.0000 chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 = 0.5030 r_free = 0.5030 target = 0.281473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.245803 restraints weight = 9443.412| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 3.48 r_work: 0.4311 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.186 4966 Z= 0.325 Angle : 0.866 11.661 7079 Z= 0.493 Chirality : 0.055 0.281 857 Planarity : 0.005 0.047 632 Dihedral : 23.171 141.556 1622 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.69 % Favored : 95.06 % Rotamer: Outliers : 2.92 % Allowed : 14.87 % Favored : 82.22 % 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: 0.44 (0.44), residues: 405 helix: -0.02 (1.48), residues: 11 sheet: 1.51 (0.43), residues: 172 loop : -0.72 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 87 TYR 0.012 0.001 TYR A 60 PHE 0.017 0.002 PHE A 178 TRP 0.008 0.001 TRP C 90 HIS 0.010 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.33 ( 4966) covalent geometry : angle 0.86633 / 0.49 ( 7079) hydrogen bonds : bond 0.11770 / 8.00 ( 185) hydrogen bonds : angle 4.60208 / 3.37 ( 435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 13 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: B 36 MET cc_start: 0.3147 (mmm) cc_final: 0.2842 (mmm) outliers start: 10 outliers final: 8 residues processed: 22 average time/residue: 0.0933 time to fit residues: 2.6891 Evaluate side-chains 21 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain C residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 50.0000 chunk 20 optimal weight: 40.0000 chunk 2 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 0.0980 chunk 18 optimal weight: 40.0000 chunk 29 optimal weight: 9.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- 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 = 0.5028 r_free = 0.5028 target = 0.281467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.233912 restraints weight = 9459.640| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 5.80 r_work: 0.4254 rms_B_bonded: 5.68 restraints_weight: 2.0000 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 4966 Z= 0.299 Angle : 0.795 9.812 7079 Z= 0.453 Chirality : 0.053 0.338 857 Planarity : 0.005 0.043 632 Dihedral : 22.826 141.791 1622 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.69 % Favored : 95.06 % Rotamer: Outliers : 2.62 % Allowed : 15.45 % Favored : 81.92 % 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: 0.61 (0.44), residues: 405 helix: 0.72 (1.51), residues: 11 sheet: 1.54 (0.43), residues: 172 loop : -0.57 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 87 TYR 0.011 0.001 TYR A 60 PHE 0.015 0.002 PHE A 178 TRP 0.007 0.001 TRP C 90 HIS 0.007 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.30 ( 4966) covalent geometry : angle 0.79523 / 0.45 ( 7079) hydrogen bonds : bond 0.10763 / 7.17 ( 185) hydrogen bonds : angle 4.36659 / 3.22 ( 435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1456.32 seconds wall clock time: 25 minutes 38.60 seconds (1538.60 seconds total)