Starting phenix.real_space_refine on Tue Jan 14 04:07:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a03_15046/01_2025/8a03_15046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a03_15046/01_2025/8a03_15046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a03_15046/01_2025/8a03_15046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a03_15046/01_2025/8a03_15046.map" model { file = "/net/cci-nas-00/data/ceres_data/8a03_15046/01_2025/8a03_15046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a03_15046/01_2025/8a03_15046.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Restraints were copied for chains: J, L Time building chain proxies: 3.14, per 1000 atoms: 0.57 Number of scatterers: 5511 At special positions: 0 Unit cell: (96.72, 101.68, 57.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1116 8.00 N 885 7.00 C 3495 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: 1.18 Conformation dependent library (CDL) restraints added in 663.6 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 18 sheets defined 10.5% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'L' and resid 60 through 66 Processing helix chain 'L' and resid 178 through 190 removed outlier: 3.686A pdb=" N ILE L 189 " --> pdb=" O LEU L 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 35 Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'K' and resid 178 through 190 removed outlier: 3.687A pdb=" N ILE K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'J' and resid 60 through 66 Processing helix chain 'J' and resid 178 through 190 removed outlier: 3.686A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 2 through 7 removed outlier: 5.738A pdb=" N LYS L 2 " --> pdb=" O GLY L 119 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY L 119 " --> pdb=" O LYS L 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L 4 " --> pdb=" O LEU L 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 15 through 17 removed outlier: 7.221A pdb=" N ILE L 40 " --> pdb=" O ASN L 56 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN L 56 " --> pdb=" O ILE L 40 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE L 42 " --> pdb=" O LEU L 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 93 through 94 removed outlier: 5.139A pdb=" N SER L 93 " --> pdb=" O THR L 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 128 through 137 removed outlier: 5.323A pdb=" N ASN L 230 " --> pdb=" O THR L 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG L 234 " --> pdb=" O LEU L 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU L 153 " --> pdb=" O ARG L 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 143 through 147 removed outlier: 6.679A pdb=" N GLN L 168 " --> pdb=" O VAL L 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE L 219 " --> pdb=" O SER L 166 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER L 166 " --> pdb=" O ILE L 219 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE L 221 " --> pdb=" O ASP L 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP L 164 " --> pdb=" O ILE L 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS L 223 " --> pdb=" O VAL L 162 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL L 162 " --> pdb=" O LYS L 223 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL L 175 " --> pdb=" O TYR L 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 194 through 195 Processing sheet with id=AA7, first strand: chain 'K' and resid 2 through 7 removed outlier: 5.738A pdb=" N LYS K 2 " --> pdb=" O GLY K 119 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY K 119 " --> pdb=" O LYS K 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA K 4 " --> pdb=" O LEU K 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 15 through 17 removed outlier: 7.220A pdb=" N ILE K 40 " --> pdb=" O ASN K 56 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN K 56 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE K 42 " --> pdb=" O LEU K 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 93 through 94 removed outlier: 5.137A pdb=" N SER K 93 " --> pdb=" O THR K 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 128 through 137 removed outlier: 5.323A pdb=" N ASN K 230 " --> pdb=" O THR K 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG K 234 " --> pdb=" O LEU K 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU K 153 " --> pdb=" O ARG K 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 143 through 147 removed outlier: 6.679A pdb=" N GLN K 168 " --> pdb=" O VAL K 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE K 219 " --> pdb=" O SER K 166 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER K 166 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE K 221 " --> pdb=" O ASP K 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP K 164 " --> pdb=" O ILE K 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS K 223 " --> pdb=" O VAL K 162 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL K 162 " --> pdb=" O LYS K 223 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL K 175 " --> pdb=" O TYR K 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'J' and resid 2 through 7 removed outlier: 5.738A pdb=" N LYS J 2 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY J 119 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 4 " --> pdb=" O LEU J 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 15 through 17 removed outlier: 7.220A pdb=" N ILE J 40 " --> pdb=" O ASN J 56 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN J 56 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE J 42 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 93 through 94 removed outlier: 5.138A pdb=" N SER J 93 " --> pdb=" O THR J 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'J' and resid 128 through 137 removed outlier: 5.323A pdb=" N ASN J 230 " --> pdb=" O THR J 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG J 234 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU J 153 " --> pdb=" O ARG J 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 143 through 147 removed outlier: 6.678A pdb=" N GLN J 168 " --> pdb=" O VAL J 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE J 219 " --> pdb=" O SER J 166 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER J 166 " --> pdb=" O ILE J 219 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE J 221 " --> pdb=" O ASP J 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP J 164 " --> pdb=" O ILE J 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS J 223 " --> pdb=" O VAL J 162 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL J 162 " --> pdb=" O LYS J 223 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL J 175 " --> pdb=" O TYR J 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 194 through 195 210 hydrogen bonds defined for protein. 540 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: 1.88 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1818 1.34 - 1.46: 1003 1.46 - 1.57: 2726 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" C VAL K 148 " pdb=" O VAL K 148 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 7.90e-01 bond pdb=" C VAL L 148 " pdb=" O VAL L 148 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.73e-01 bond pdb=" C VAL J 148 " pdb=" O VAL J 148 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.54e-01 bond pdb=" CG LEU K 117 " pdb=" CD2 LEU K 117 " ideal model delta sigma weight residual 1.521 1.503 0.018 3.30e-02 9.18e+02 2.81e-01 bond pdb=" CG LEU J 117 " pdb=" CD2 LEU J 117 " ideal model delta sigma weight residual 1.521 1.504 0.017 3.30e-02 9.18e+02 2.80e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 7232 0.91 - 1.81: 242 1.81 - 2.72: 48 2.72 - 3.63: 23 3.63 - 4.53: 3 Bond angle restraints: 7548 Sorted by residual: angle pdb=" C LEU L 26 " pdb=" N SER L 27 " pdb=" CA SER L 27 " ideal model delta sigma weight residual 122.73 120.05 2.68 1.62e+00 3.81e-01 2.73e+00 angle pdb=" C LEU J 26 " pdb=" N SER J 27 " pdb=" CA SER J 27 " ideal model delta sigma weight residual 122.73 120.08 2.65 1.62e+00 3.81e-01 2.69e+00 angle pdb=" C LEU K 26 " pdb=" N SER K 27 " pdb=" CA SER K 27 " ideal model delta sigma weight residual 122.73 120.11 2.62 1.62e+00 3.81e-01 2.61e+00 angle pdb=" CA LEU K 26 " pdb=" CB LEU K 26 " pdb=" CG LEU K 26 " ideal model delta sigma weight residual 116.30 120.83 -4.53 3.50e+00 8.16e-02 1.68e+00 angle pdb=" CA LEU L 26 " pdb=" CB LEU L 26 " pdb=" CG LEU L 26 " ideal model delta sigma weight residual 116.30 120.81 -4.51 3.50e+00 8.16e-02 1.66e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3108 17.97 - 35.94: 246 35.94 - 53.91: 45 53.91 - 71.87: 18 71.87 - 89.84: 3 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CA GLN J 75 " pdb=" CB GLN J 75 " pdb=" CG GLN J 75 " pdb=" CD GLN J 75 " ideal model delta sinusoidal sigma weight residual -60.00 -106.76 46.76 3 1.50e+01 4.44e-03 8.39e+00 dihedral pdb=" CA GLN L 75 " pdb=" CB GLN L 75 " pdb=" CG GLN L 75 " pdb=" CD GLN L 75 " ideal model delta sinusoidal sigma weight residual -60.00 -106.73 46.73 3 1.50e+01 4.44e-03 8.38e+00 dihedral pdb=" CA GLN K 75 " pdb=" CB GLN K 75 " pdb=" CG GLN K 75 " pdb=" CD GLN K 75 " ideal model delta sinusoidal sigma weight residual -60.00 -106.68 46.68 3 1.50e+01 4.44e-03 8.37e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 593 0.027 - 0.054: 173 0.054 - 0.081: 59 0.081 - 0.108: 76 0.108 - 0.135: 35 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE K 42 " pdb=" N ILE K 42 " pdb=" C ILE K 42 " pdb=" CB ILE K 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE J 42 " pdb=" N ILE J 42 " pdb=" C ILE J 42 " pdb=" CB ILE J 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE L 42 " pdb=" N ILE L 42 " pdb=" C ILE L 42 " pdb=" CB ILE L 42 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU J 178 " 0.015 5.00e-02 4.00e+02 2.20e-02 7.77e-01 pdb=" N PRO J 179 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO J 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 179 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 178 " 0.014 5.00e-02 4.00e+02 2.18e-02 7.62e-01 pdb=" N PRO K 179 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO K 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 179 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 178 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.60e-01 pdb=" N PRO L 179 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO L 179 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO L 179 " -0.012 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2046 2.90 - 3.40: 4445 3.40 - 3.90: 8664 3.90 - 4.40: 9263 4.40 - 4.90: 17482 Nonbonded interactions: 41900 Sorted by model distance: nonbonded pdb=" N GLY J 22 " pdb=" O ILE J 120 " model vdw 2.399 3.120 nonbonded pdb=" N GLY L 22 " pdb=" O ILE L 120 " model vdw 2.399 3.120 nonbonded pdb=" N GLY K 22 " pdb=" O ILE K 120 " model vdw 2.399 3.120 nonbonded pdb=" N ASP J 207 " pdb=" OD1 ASP J 207 " model vdw 2.421 3.120 nonbonded pdb=" N ASP L 207 " pdb=" OD1 ASP L 207 " model vdw 2.422 3.120 ... (remaining 41895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } 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: 0.340 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.160 Find NCS groups from input model: 0.120 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5571 Z= 0.110 Angle : 0.437 4.533 7548 Z= 0.231 Chirality : 0.044 0.135 936 Planarity : 0.002 0.022 960 Dihedral : 14.179 89.842 2064 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.33), residues: 711 helix: 1.61 (0.71), residues: 66 sheet: 1.39 (0.31), residues: 315 loop : -0.85 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 118 PHE 0.004 0.001 PHE L 231 TYR 0.005 0.001 TYR L 43 ARG 0.003 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.634 Fit side-chains REVERT: L 38 GLU cc_start: 0.8123 (mp0) cc_final: 0.7697 (mp0) REVERT: L 122 GLU cc_start: 0.7407 (pt0) cc_final: 0.7192 (pt0) REVERT: L 152 ASP cc_start: 0.7491 (p0) cc_final: 0.7201 (p0) REVERT: K 100 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7666 (mt-10) REVERT: J 101 SER cc_start: 0.8415 (m) cc_final: 0.8003 (p) REVERT: J 152 ASP cc_start: 0.7273 (p0) cc_final: 0.7040 (p0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1566 time to fit residues: 24.2789 Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.0010 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN L 225 GLN K 225 GLN J 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100067 restraints weight = 7602.685| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.04 r_work: 0.2991 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5571 Z= 0.248 Angle : 0.518 5.147 7548 Z= 0.275 Chirality : 0.047 0.146 936 Planarity : 0.003 0.030 960 Dihedral : 3.680 10.710 750 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.90 % Allowed : 6.67 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.33), residues: 711 helix: 0.65 (0.65), residues: 72 sheet: 1.38 (0.32), residues: 312 loop : -0.98 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.008 0.001 PHE J 142 TYR 0.019 0.002 TYR L 43 ARG 0.006 0.001 ARG K 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.668 Fit side-chains REVERT: L 152 ASP cc_start: 0.8060 (p0) cc_final: 0.7825 (p0) REVERT: J 101 SER cc_start: 0.8594 (m) cc_final: 0.8182 (p) outliers start: 12 outliers final: 11 residues processed: 77 average time/residue: 0.1342 time to fit residues: 14.5860 Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 168 GLN Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 GLN L 134 GLN K 75 GLN J 16 GLN J 75 GLN J 134 GLN J 225 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099468 restraints weight = 7706.470| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.01 r_work: 0.2977 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5571 Z= 0.315 Angle : 0.547 4.913 7548 Z= 0.292 Chirality : 0.048 0.148 936 Planarity : 0.003 0.035 960 Dihedral : 4.047 13.253 750 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.22 % Allowed : 11.43 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.32), residues: 711 helix: 0.20 (0.62), residues: 72 sheet: 1.28 (0.32), residues: 306 loop : -1.18 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 118 PHE 0.008 0.001 PHE J 142 TYR 0.013 0.001 TYR L 43 ARG 0.007 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.690 Fit side-chains REVERT: L 146 ILE cc_start: 0.8439 (pt) cc_final: 0.8100 (mt) REVERT: L 168 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: J 101 SER cc_start: 0.8674 (m) cc_final: 0.8290 (p) REVERT: J 140 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8465 (mp0) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.1272 time to fit residues: 13.6614 Evaluate side-chains 61 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 75 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 75 GLN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 7 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102065 restraints weight = 7698.755| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.04 r_work: 0.2988 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5571 Z= 0.117 Angle : 0.439 3.855 7548 Z= 0.238 Chirality : 0.046 0.132 936 Planarity : 0.003 0.025 960 Dihedral : 3.584 12.207 750 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.75 % Allowed : 11.90 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.33), residues: 711 helix: 0.79 (0.66), residues: 72 sheet: 1.37 (0.32), residues: 306 loop : -1.13 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 118 PHE 0.004 0.001 PHE J 231 TYR 0.013 0.001 TYR L 43 ARG 0.005 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.607 Fit side-chains REVERT: J 101 SER cc_start: 0.8627 (m) cc_final: 0.8168 (p) REVERT: J 140 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8473 (mp0) REVERT: J 149 GLN cc_start: 0.8126 (tt0) cc_final: 0.7905 (tt0) outliers start: 11 outliers final: 9 residues processed: 75 average time/residue: 0.1130 time to fit residues: 12.6877 Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.093541 restraints weight = 7882.492| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.02 r_work: 0.2878 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 5571 Z= 0.590 Angle : 0.697 5.859 7548 Z= 0.366 Chirality : 0.053 0.170 936 Planarity : 0.004 0.040 960 Dihedral : 4.633 15.080 750 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.54 % Allowed : 13.97 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.31), residues: 711 helix: -0.21 (0.61), residues: 72 sheet: 0.92 (0.31), residues: 312 loop : -1.50 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS L 118 PHE 0.010 0.002 PHE K 142 TYR 0.018 0.002 TYR L 43 ARG 0.004 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.683 Fit side-chains REVERT: L 101 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8388 (p) REVERT: L 165 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8392 (tt) REVERT: K 227 SER cc_start: 0.8780 (t) cc_final: 0.8539 (m) REVERT: J 101 SER cc_start: 0.8855 (m) cc_final: 0.8445 (p) REVERT: J 107 GLU cc_start: 0.8618 (tp30) cc_final: 0.8389 (tp30) outliers start: 16 outliers final: 11 residues processed: 69 average time/residue: 0.1315 time to fit residues: 12.9316 Evaluate side-chains 63 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101191 restraints weight = 7642.065| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.90 r_work: 0.2969 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5571 Z= 0.129 Angle : 0.446 3.827 7548 Z= 0.244 Chirality : 0.046 0.134 936 Planarity : 0.003 0.025 960 Dihedral : 3.766 13.495 750 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.11 % Allowed : 15.24 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.32), residues: 711 helix: 0.56 (0.65), residues: 72 sheet: 1.12 (0.32), residues: 306 loop : -1.30 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS L 118 PHE 0.004 0.001 PHE J 231 TYR 0.019 0.001 TYR L 43 ARG 0.004 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.605 Fit side-chains REVERT: L 101 SER cc_start: 0.8694 (m) cc_final: 0.8335 (p) REVERT: L 168 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: J 101 SER cc_start: 0.8664 (m) cc_final: 0.8278 (p) REVERT: J 149 GLN cc_start: 0.8162 (tt0) cc_final: 0.7954 (tt0) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.1323 time to fit residues: 11.0355 Evaluate side-chains 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 0.0040 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.094698 restraints weight = 7942.339| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.93 r_work: 0.2893 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 5571 Z= 0.487 Angle : 0.629 5.063 7548 Z= 0.333 Chirality : 0.050 0.144 936 Planarity : 0.004 0.037 960 Dihedral : 4.501 14.913 750 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.86 % Allowed : 14.13 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.31), residues: 711 helix: -0.13 (0.62), residues: 72 sheet: 0.90 (0.32), residues: 306 loop : -1.55 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 118 PHE 0.008 0.001 PHE K 142 TYR 0.018 0.002 TYR L 43 ARG 0.004 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.603 Fit side-chains REVERT: L 101 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8439 (p) REVERT: L 165 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8410 (tt) REVERT: L 168 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: K 101 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8426 (p) REVERT: K 227 SER cc_start: 0.8796 (t) cc_final: 0.8551 (m) REVERT: J 101 SER cc_start: 0.8809 (m) cc_final: 0.8435 (p) REVERT: J 107 GLU cc_start: 0.8424 (tp30) cc_final: 0.8187 (tp30) outliers start: 18 outliers final: 9 residues processed: 65 average time/residue: 0.1226 time to fit residues: 11.8299 Evaluate side-chains 61 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.351 > 50: distance: 17 - 22: 15.748 distance: 22 - 23: 21.830 distance: 23 - 24: 21.894 distance: 23 - 26: 22.340 distance: 24 - 25: 11.981 distance: 24 - 29: 6.555 distance: 26 - 27: 20.789 distance: 26 - 28: 26.335 distance: 29 - 30: 10.815 distance: 30 - 31: 18.172 distance: 30 - 33: 26.615 distance: 31 - 32: 36.645 distance: 31 - 38: 19.592 distance: 33 - 34: 27.958 distance: 34 - 35: 7.541 distance: 35 - 36: 18.106 distance: 36 - 37: 22.222 distance: 38 - 39: 17.872 distance: 39 - 40: 37.078 distance: 39 - 42: 22.726 distance: 40 - 41: 30.561 distance: 40 - 44: 15.196 distance: 42 - 43: 5.736 distance: 44 - 45: 30.173 distance: 44 - 50: 31.759 distance: 45 - 46: 26.488 distance: 45 - 48: 18.977 distance: 46 - 47: 40.987 distance: 46 - 51: 19.294 distance: 48 - 49: 7.849 distance: 49 - 50: 32.410 distance: 51 - 52: 13.222 distance: 52 - 53: 13.594 distance: 52 - 55: 8.440 distance: 53 - 54: 13.895 distance: 53 - 60: 23.292 distance: 55 - 56: 14.836 distance: 56 - 57: 14.848 distance: 57 - 58: 5.849 distance: 57 - 59: 9.806 distance: 60 - 61: 11.064 distance: 60 - 143: 19.209 distance: 61 - 62: 15.304 distance: 61 - 64: 22.201 distance: 62 - 63: 28.251 distance: 62 - 68: 15.605 distance: 63 - 140: 23.878 distance: 64 - 65: 11.555 distance: 65 - 66: 11.332 distance: 65 - 67: 12.018 distance: 68 - 69: 20.278 distance: 69 - 70: 44.055 distance: 69 - 72: 19.436 distance: 70 - 71: 20.000 distance: 70 - 77: 46.423 distance: 72 - 73: 28.021 distance: 74 - 75: 11.465 distance: 74 - 76: 18.179 distance: 77 - 78: 51.514 distance: 77 - 126: 28.308 distance: 78 - 79: 33.753 distance: 78 - 81: 37.965 distance: 79 - 80: 19.110 distance: 79 - 84: 22.023 distance: 80 - 123: 16.170 distance: 81 - 82: 29.574 distance: 81 - 83: 30.385 distance: 84 - 85: 9.260 distance: 85 - 88: 12.181 distance: 86 - 87: 18.238 distance: 86 - 91: 12.992 distance: 88 - 89: 8.500 distance: 88 - 90: 14.506 distance: 91 - 92: 6.900 distance: 92 - 93: 9.765 distance: 92 - 95: 6.565 distance: 93 - 94: 16.725 distance: 93 - 100: 15.904 distance: 95 - 96: 9.311 distance: 96 - 97: 7.098 distance: 97 - 98: 8.690 distance: 98 - 99: 9.356