Starting phenix.real_space_refine on Wed Jul 1 22:41:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrw_37792/07_2026/8wrw_37792.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrw_37792/07_2026/8wrw_37792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrw_37792/07_2026/8wrw_37792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrw_37792/07_2026/8wrw_37792.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrw_37792/07_2026/8wrw_37792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrw_37792/07_2026/8wrw_37792.cif" } resolution = 3.01 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= 0.001 sd= 0.014 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 74 5.49 5 S 3 5.16 5 C 2070 2.51 5 N 666 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 3671 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2127 Classifications: {'peptide': 270} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 243} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 562 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 843 Classifications: {'RNA': 40} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 16, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 33} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 1.11, per 1000 atoms: 0.30 Number of scatterers: 3671 At special positions: 0 Unit cell: (64.02, 102.3, 90.42, 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 3 16.00 P 74 15.00 O 858 8.00 N 666 7.00 C 2070 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: 0.46 Conformation dependent library (CDL) restraints added in 64.8 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 41.5% alpha, 8.1% beta 6 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.601A pdb=" N TYR A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.170A pdb=" N GLU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.019A pdb=" N LEU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 131 through 169 removed outlier: 3.977A pdb=" N PHE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 308 through 318 removed outlier: 4.205A pdb=" N LEU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 4.063A pdb=" N LEU A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 7.215A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 446 1.32 - 1.44: 1448 1.44 - 1.56: 1861 1.56 - 1.68: 145 1.68 - 1.80: 4 Bond restraints: 3904 Sorted by residual: bond pdb=" C3' DT C 4 " pdb=" C2' DT C 4 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C1' DT C -18 " pdb=" N1 DT C -18 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.15e+01 bond pdb=" C3' DG C -12 " pdb=" C2' DG C -12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C ALA A 309 " pdb=" O ALA A 309 " ideal model delta sigma weight residual 1.236 1.194 0.041 1.35e-02 5.49e+03 9.38e+00 bond pdb=" C3' DA D -4 " pdb=" C2' DA D -4 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.87e+00 ... (remaining 3899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5378 1.99 - 3.98: 214 3.98 - 5.96: 13 5.96 - 7.95: 9 7.95 - 9.94: 4 Bond angle restraints: 5618 Sorted by residual: angle pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sigma weight residual 117.70 122.97 -5.27 1.20e+00 6.94e-01 1.93e+01 angle pdb=" N3 DT C -7 " pdb=" C4 DT C -7 " pdb=" O4 DT C -7 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT C -19 " pdb=" C4 DT C -19 " pdb=" O4 DT C -19 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 ... (remaining 5613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 2088 35.01 - 70.01: 213 70.01 - 105.01: 19 105.01 - 140.02: 0 140.02 - 175.02: 2 Dihedral angle restraints: 2322 sinusoidal: 1563 harmonic: 759 Sorted by residual: dihedral pdb=" O4' U B 10 " pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sinusoidal sigma weight residual 200.00 24.98 175.02 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 59.50 172.50 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' A B 18 " pdb=" C1' A B 18 " pdb=" N9 A B 18 " pdb=" C4 A B 18 " ideal model delta sinusoidal sigma weight residual -90.00 -18.81 -71.19 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 2319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 484 0.051 - 0.102: 131 0.102 - 0.153: 27 0.153 - 0.204: 4 0.204 - 0.255: 3 Chirality restraints: 649 Sorted by residual: chirality pdb=" CA ARG A 106 " pdb=" N ARG A 106 " pdb=" C ARG A 106 " pdb=" CB ARG A 106 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ALA A 309 " pdb=" N ALA A 309 " pdb=" C ALA A 309 " pdb=" CB ALA A 309 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASP A 101 " pdb=" N ASP A 101 " pdb=" C ASP A 101 " pdb=" CB ASP A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 646 not shown) Planarity restraints: 455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 228 " -0.055 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO A 229 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 305 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C ILE A 305 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 305 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 306 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 302 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C LYS A 302 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS A 302 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP A 303 " 0.011 2.00e-02 2.50e+03 ... (remaining 452 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 915 2.80 - 3.33: 3194 3.33 - 3.85: 6561 3.85 - 4.38: 7984 4.38 - 4.90: 11406 Nonbonded interactions: 30060 Sorted by model distance: nonbonded pdb=" O2' U B -10 " pdb=" O2 U B -9 " model vdw 2.277 3.040 nonbonded pdb=" NE ARG A 314 " pdb=" O4 U B -17 " model vdw 2.284 3.120 nonbonded pdb=" NH2 ARG A 271 " pdb=" N7 G B -12 " model vdw 2.360 3.200 nonbonded pdb=" N2 DG C -5 " pdb=" O2 C B 5 " model vdw 2.371 3.120 nonbonded pdb=" N1 DG C -5 " pdb=" N3 C B 5 " model vdw 2.420 3.200 ... (remaining 30055 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.550 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 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 0.047 3904 Z= 0.421 Angle : 0.862 9.937 5618 Z= 0.617 Chirality : 0.050 0.255 649 Planarity : 0.008 0.084 455 Dihedral : 22.604 175.022 1836 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.70 % Allowed : 3.60 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.53), residues: 256 helix: -0.61 (0.55), residues: 85 sheet: -2.29 (0.86), residues: 32 loop : -0.61 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 134 TYR 0.008 0.002 TYR A 201 PHE 0.023 0.003 PHE A 102 TRP 0.011 0.002 TRP A 318 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.42 ( 3904) covalent geometry : angle 0.86181 / 0.62 ( 5618) hydrogen bonds : bond 0.27591 / 19.74 ( 92) hydrogen bonds : angle 10.91401 / 7.77 ( 236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.119 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 34 average time/residue: 0.1219 time to fit residues: 4.8945 Evaluate side-chains 28 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 203 GLN A 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.202566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.171143 restraints weight = 5158.155| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.19 r_work: 0.4097 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3904 Z= 0.207 Angle : 0.685 8.560 5618 Z= 0.382 Chirality : 0.044 0.240 649 Planarity : 0.007 0.062 455 Dihedral : 24.654 179.716 1310 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.70 % Allowed : 6.76 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.54), residues: 256 helix: -0.81 (0.52), residues: 97 sheet: -2.19 (0.85), residues: 32 loop : -0.40 (0.61), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 134 TYR 0.010 0.002 TYR A 201 PHE 0.013 0.002 PHE A 102 TRP 0.012 0.002 TRP A 249 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.21 ( 3904) covalent geometry : angle 0.68491 / 0.38 ( 5618) hydrogen bonds : bond 0.08260 / 6.13 ( 92) hydrogen bonds : angle 6.73258 / 4.88 ( 236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 112 TRP cc_start: 0.5880 (t60) cc_final: 0.5622 (t60) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.0968 time to fit residues: 3.9195 Evaluate side-chains 33 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 0.0980 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.3278 ------------------------------------------------------------------------------- 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 = 0.4591 r_free = 0.4591 target = 0.205128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.172195 restraints weight = 5103.783| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.25 r_work: 0.4112 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3904 Z= 0.163 Angle : 0.586 6.054 5618 Z= 0.336 Chirality : 0.040 0.194 649 Planarity : 0.006 0.051 455 Dihedral : 24.545 179.733 1309 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.25 % Allowed : 14.41 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.54), residues: 256 helix: -0.71 (0.50), residues: 97 sheet: -1.94 (0.86), residues: 32 loop : -0.26 (0.63), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 276 TYR 0.013 0.002 TYR A 209 PHE 0.010 0.001 PHE A 102 TRP 0.010 0.002 TRP A 249 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 ( 3904) covalent geometry : angle 0.58563 / 0.34 ( 5618) hydrogen bonds : bond 0.06695 / 4.83 ( 92) hydrogen bonds : angle 5.93624 / 4.21 ( 236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 112 TRP cc_start: 0.5839 (t60) cc_final: 0.5574 (t60) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.1058 time to fit residues: 4.2763 Evaluate side-chains 34 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 21 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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 = 0.4595 r_free = 0.4595 target = 0.204253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173068 restraints weight = 5175.505| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 1.18 r_work: 0.4130 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3904 Z= 0.154 Angle : 0.571 6.381 5618 Z= 0.326 Chirality : 0.039 0.181 649 Planarity : 0.006 0.044 455 Dihedral : 24.398 179.882 1308 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.25 % Allowed : 17.57 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.55), residues: 256 helix: -0.60 (0.51), residues: 97 sheet: -1.79 (0.83), residues: 38 loop : -0.21 (0.64), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 276 TYR 0.010 0.002 TYR A 140 PHE 0.014 0.002 PHE A 335 TRP 0.010 0.001 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 3904) covalent geometry : angle 0.57059 / 0.33 ( 5618) hydrogen bonds : bond 0.05533 / 3.84 ( 92) hydrogen bonds : angle 5.43637 / 3.75 ( 236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 112 TRP cc_start: 0.5847 (t60) cc_final: 0.5539 (t60) REVERT: A 202 GLN cc_start: 0.6921 (tt0) cc_final: 0.6625 (tt0) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.0942 time to fit residues: 4.2274 Evaluate side-chains 39 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.4570 r_free = 0.4570 target = 0.202011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.170257 restraints weight = 5152.109| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.17 r_work: 0.4092 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 3904 Z= 0.198 Angle : 0.619 6.938 5618 Z= 0.349 Chirality : 0.042 0.175 649 Planarity : 0.006 0.047 455 Dihedral : 24.478 179.834 1308 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.60 % Allowed : 18.47 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.53), residues: 256 helix: -0.65 (0.51), residues: 99 sheet: -1.95 (0.83), residues: 38 loop : -0.45 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.010 0.002 TYR A 209 PHE 0.008 0.002 PHE A 102 TRP 0.013 0.002 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 ( 3904) covalent geometry : angle 0.61934 / 0.35 ( 5618) hydrogen bonds : bond 0.06440 / 4.50 ( 92) hydrogen bonds : angle 5.41431 / 3.73 ( 236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.101 Fit side-chains REVERT: A 112 TRP cc_start: 0.5979 (t60) cc_final: 0.5618 (t60) outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 0.1059 time to fit residues: 4.6023 Evaluate side-chains 38 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.0670 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.202013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.170332 restraints weight = 5181.721| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.17 r_work: 0.4092 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3904 Z= 0.197 Angle : 0.617 7.223 5618 Z= 0.348 Chirality : 0.043 0.171 649 Planarity : 0.006 0.045 455 Dihedral : 24.507 179.884 1308 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.60 % Allowed : 18.02 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.52), residues: 256 helix: -0.85 (0.49), residues: 99 sheet: -1.86 (0.84), residues: 38 loop : -0.55 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 134 TYR 0.011 0.002 TYR A 209 PHE 0.009 0.002 PHE A 102 TRP 0.012 0.002 TRP A 249 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 ( 3904) covalent geometry : angle 0.61741 / 0.35 ( 5618) hydrogen bonds : bond 0.06016 / 4.27 ( 92) hydrogen bonds : angle 5.43007 / 3.77 ( 236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.096 Fit side-chains REVERT: A 112 TRP cc_start: 0.5972 (t60) cc_final: 0.5570 (t60) outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 0.1016 time to fit residues: 4.4221 Evaluate side-chains 38 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 0.0870 overall best weight: 0.2356 ------------------------------------------------------------------------------- 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 = 0.4593 r_free = 0.4593 target = 0.204370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.173131 restraints weight = 5304.397| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 1.17 r_work: 0.4126 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4000 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3904 Z= 0.144 Angle : 0.556 6.722 5618 Z= 0.318 Chirality : 0.039 0.157 649 Planarity : 0.006 0.038 455 Dihedral : 24.465 179.770 1308 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.80 % Allowed : 18.92 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.53), residues: 256 helix: -0.37 (0.52), residues: 93 sheet: -1.73 (0.82), residues: 38 loop : -0.47 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 134 TYR 0.011 0.002 TYR A 209 PHE 0.009 0.001 PHE A 334 TRP 0.011 0.001 TRP A 112 HIS 0.001 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 3904) covalent geometry : angle 0.55590 / 0.32 ( 5618) hydrogen bonds : bond 0.05058 / 3.52 ( 92) hydrogen bonds : angle 5.21433 / 3.55 ( 236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 112 TRP cc_start: 0.5942 (t60) cc_final: 0.5526 (t60) REVERT: A 202 GLN cc_start: 0.6804 (tt0) cc_final: 0.6554 (tt0) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.1068 time to fit residues: 4.5804 Evaluate side-chains 37 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 = 0.4588 r_free = 0.4588 target = 0.203995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.172432 restraints weight = 5207.484| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.19 r_work: 0.4116 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3992 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3904 Z= 0.155 Angle : 0.560 6.345 5618 Z= 0.319 Chirality : 0.039 0.153 649 Planarity : 0.006 0.041 455 Dihedral : 24.453 178.982 1308 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.70 % Allowed : 18.47 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.53), residues: 256 helix: -0.30 (0.52), residues: 93 sheet: -1.88 (0.80), residues: 38 loop : -0.53 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 134 TYR 0.009 0.002 TYR A 201 PHE 0.008 0.001 PHE A 102 TRP 0.010 0.002 TRP A 112 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 3904) covalent geometry : angle 0.55983 / 0.32 ( 5618) hydrogen bonds : bond 0.05138 / 3.53 ( 92) hydrogen bonds : angle 5.09739 / 3.48 ( 236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.097 Fit side-chains REVERT: A 112 TRP cc_start: 0.5936 (t60) cc_final: 0.5524 (t60) REVERT: A 202 GLN cc_start: 0.6805 (tt0) cc_final: 0.6591 (tt0) outliers start: 6 outliers final: 6 residues processed: 37 average time/residue: 0.1040 time to fit residues: 4.5127 Evaluate side-chains 39 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4577 r_free = 0.4577 target = 0.202995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.171230 restraints weight = 5199.995| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.19 r_work: 0.4097 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3968 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3904 Z= 0.176 Angle : 0.586 6.450 5618 Z= 0.331 Chirality : 0.041 0.157 649 Planarity : 0.006 0.045 455 Dihedral : 24.489 179.096 1308 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.70 % Allowed : 18.92 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.53), residues: 256 helix: -0.29 (0.52), residues: 93 sheet: -1.99 (0.80), residues: 38 loop : -0.56 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 134 TYR 0.010 0.002 TYR A 209 PHE 0.007 0.001 PHE A 350 TRP 0.011 0.002 TRP A 249 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 ( 3904) covalent geometry : angle 0.58590 / 0.33 ( 5618) hydrogen bonds : bond 0.05388 / 3.73 ( 92) hydrogen bonds : angle 5.13623 / 3.52 ( 236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.092 Fit side-chains REVERT: A 112 TRP cc_start: 0.5926 (t60) cc_final: 0.5551 (t60) outliers start: 6 outliers final: 6 residues processed: 37 average time/residue: 0.0887 time to fit residues: 3.8085 Evaluate side-chains 40 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.0030 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.0070 chunk 0 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 overall best weight: 0.2608 ------------------------------------------------------------------------------- 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 = 0.4594 r_free = 0.4594 target = 0.204649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.173249 restraints weight = 5273.924| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 1.18 r_work: 0.4126 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3904 Z= 0.141 Angle : 0.549 6.167 5618 Z= 0.313 Chirality : 0.038 0.151 649 Planarity : 0.006 0.039 455 Dihedral : 24.476 179.438 1308 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.70 % Allowed : 19.37 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.53), residues: 256 helix: -0.29 (0.52), residues: 95 sheet: -1.89 (0.81), residues: 38 loop : -0.39 (0.60), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 134 TYR 0.009 0.002 TYR A 209 PHE 0.007 0.001 PHE A 102 TRP 0.011 0.001 TRP A 112 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 3904) covalent geometry : angle 0.54878 / 0.31 ( 5618) hydrogen bonds : bond 0.04782 / 3.29 ( 92) hydrogen bonds : angle 5.02875 / 3.45 ( 236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.058 Fit side-chains REVERT: A 112 TRP cc_start: 0.5911 (t60) cc_final: 0.5524 (t60) outliers start: 6 outliers final: 6 residues processed: 37 average time/residue: 0.0991 time to fit residues: 4.2596 Evaluate side-chains 38 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 13 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.201773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.170127 restraints weight = 5105.269| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.17 r_work: 0.4084 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3904 Z= 0.214 Angle : 0.634 7.229 5618 Z= 0.353 Chirality : 0.043 0.164 649 Planarity : 0.006 0.048 455 Dihedral : 24.568 179.441 1308 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.15 % Allowed : 19.37 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.52), residues: 256 helix: -0.45 (0.52), residues: 95 sheet: -2.14 (0.79), residues: 38 loop : -0.52 (0.59), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 134 TYR 0.011 0.002 TYR A 209 PHE 0.005 0.001 PHE A 350 TRP 0.014 0.002 TRP A 249 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 ( 3904) covalent geometry : angle 0.63365 / 0.35 ( 5618) hydrogen bonds : bond 0.05890 / 4.12 ( 92) hydrogen bonds : angle 5.35276 / 3.69 ( 236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1462.89 seconds wall clock time: 25 minutes 40.04 seconds (1540.04 seconds total)