Starting phenix.real_space_refine on Tue Aug 4 13:54:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrw_37792/08_2026/8wrw_37792.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrw_37792/08_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_37792/08_2026/8wrw_37792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrw_37792/08_2026/8wrw_37792.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrw_37792/08_2026/8wrw_37792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrw_37792/08_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-2.2rc3-6140/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: 0.80, per 1000 atoms: 0.22 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: 0.31 Conformation dependent library (CDL) restraints added in 49.0 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: 0.43 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: 0.39 Time building geometry restraints manager: 0.41 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: 5285 1.99 - 3.98: 307 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=" O5' C B -5 " pdb=" C5' C B -5 " pdb=" C4' C B -5 " ideal model delta sigma weight residual 109.40 112.68 -3.28 8.00e-01 1.56e+00 1.68e+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 ... (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: 444 0.051 - 0.102: 138 0.102 - 0.153: 60 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.790 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- 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= 0.427 Angle : 0.924 9.937 5618 Z= 0.675 Chirality : 0.059 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 0.00539 / 0.43 ( 3904) covalent geometry : angle 0.92384 / 0.68 ( 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 : 0.093 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 34 average time/residue: 0.1037 time to fit residues: 4.1723 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 : 0.094 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 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 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.202513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.171460 restraints weight = 5158.338| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 1.13 r_work: 0.4107 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3980 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3904 Z= 0.204 Angle : 0.680 8.372 5618 Z= 0.380 Chirality : 0.043 0.145 649 Planarity : 0.007 0.063 455 Dihedral : 24.596 179.837 1310 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.70 % Allowed : 7.21 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.54), residues: 256 helix: -0.83 (0.52), residues: 97 sheet: -2.17 (0.85), residues: 32 loop : -0.39 (0.61), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 134 TYR 0.010 0.002 TYR A 209 PHE 0.012 0.002 PHE A 102 TRP 0.013 0.002 TRP A 249 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 ( 3904) covalent geometry : angle 0.68001 / 0.38 ( 5618) hydrogen bonds : bond 0.08510 / 6.29 ( 92) hydrogen bonds : angle 6.78326 / 4.92 ( 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 : 0.117 Fit side-chains revert: symmetry clash REVERT: A 112 TRP cc_start: 0.5884 (t60) cc_final: 0.5625 (t60) REVERT: A 310 ARG cc_start: 0.7459 (mtm180) cc_final: 0.7238 (mtm180) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.0997 time to fit residues: 4.0404 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 : 0.093 ------------------------------------------------------------------------------- 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: 0.0020 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 0.0980 chunk 19 optimal weight: 0.0040 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.3000 ------------------------------------------------------------------------------- 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 = 0.4594 r_free = 0.4594 target = 0.204407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.173176 restraints weight = 5218.275| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 1.18 r_work: 0.4125 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.1778 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= 0.158 Angle : 0.583 5.941 5618 Z= 0.336 Chirality : 0.039 0.138 649 Planarity : 0.006 0.050 455 Dihedral : 24.521 179.045 1309 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.80 % Allowed : 14.86 % 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: -1.12 (0.54), residues: 256 helix: -0.67 (0.51), residues: 97 sheet: -1.89 (0.86), residues: 32 loop : -0.29 (0.62), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 276 TYR 0.012 0.002 TYR A 209 PHE 0.010 0.002 PHE A 335 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 0.00301 / 0.16 ( 3904) covalent geometry : angle 0.58260 / 0.34 ( 5618) hydrogen bonds : bond 0.06436 / 4.61 ( 92) hydrogen bonds : angle 5.77795 / 4.08 ( 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 35 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: A 112 TRP cc_start: 0.5868 (t60) cc_final: 0.5617 (t60) REVERT: A 308 ASP cc_start: 0.6930 (t0) cc_final: 0.6617 (t70) outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 0.0996 time to fit residues: 3.9216 Evaluate side-chains 33 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 299 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 23 optimal weight: 0.0010 chunk 28 optimal weight: 4.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.201146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.169562 restraints weight = 5129.943| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 1.15 r_work: 0.4081 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3904 Z= 0.205 Angle : 0.641 7.234 5618 Z= 0.360 Chirality : 0.042 0.146 649 Planarity : 0.007 0.046 455 Dihedral : 24.524 179.399 1308 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.25 % Allowed : 18.02 % Favored : 79.73 % 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: -1.28 (0.54), residues: 256 helix: -0.60 (0.51), residues: 98 sheet: -2.23 (0.84), residues: 32 loop : -0.49 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.011 0.002 TYR A 209 PHE 0.010 0.002 PHE A 102 TRP 0.014 0.002 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.21 ( 3904) covalent geometry : angle 0.64119 / 0.36 ( 5618) hydrogen bonds : bond 0.06592 / 4.63 ( 92) hydrogen bonds : angle 5.75279 / 4.02 ( 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 39 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.120 Fit side-chains REVERT: A 112 TRP cc_start: 0.5883 (t60) cc_final: 0.5551 (t60) REVERT: A 308 ASP cc_start: 0.6943 (t0) cc_final: 0.6692 (t70) outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.1348 time to fit residues: 5.8012 Evaluate side-chains 39 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.0030 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.201408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.169661 restraints weight = 5142.588| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.16 r_work: 0.4083 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3904 Z= 0.192 Angle : 0.616 6.871 5618 Z= 0.349 Chirality : 0.041 0.146 649 Planarity : 0.006 0.046 455 Dihedral : 24.538 179.202 1308 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: -1.48 (0.52), residues: 256 helix: -0.87 (0.49), residues: 101 sheet: -2.03 (0.82), residues: 38 loop : -0.49 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.012 0.002 TYR A 209 PHE 0.010 0.002 PHE A 335 TRP 0.013 0.002 TRP A 249 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 3904) covalent geometry : angle 0.61592 / 0.35 ( 5618) hydrogen bonds : bond 0.06283 / 4.46 ( 92) hydrogen bonds : angle 5.65502 / 3.95 ( 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 : 0.095 Fit side-chains REVERT: A 112 TRP cc_start: 0.5904 (t60) cc_final: 0.5560 (t60) REVERT: A 308 ASP cc_start: 0.6950 (t0) cc_final: 0.6707 (t70) outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 0.1057 time to fit residues: 4.6062 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 : 0.092 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.202820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.171660 restraints weight = 5219.482| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 1.16 r_work: 0.4104 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3904 Z= 0.161 Angle : 0.579 7.433 5618 Z= 0.330 Chirality : 0.039 0.149 649 Planarity : 0.006 0.041 455 Dihedral : 24.502 179.058 1308 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.70 % Allowed : 19.82 % 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: -1.27 (0.53), residues: 256 helix: -0.67 (0.50), residues: 99 sheet: -1.87 (0.84), residues: 38 loop : -0.43 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 134 TYR 0.011 0.002 TYR A 209 PHE 0.007 0.002 PHE A 102 TRP 0.012 0.002 TRP A 112 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 3904) covalent geometry : angle 0.57865 / 0.33 ( 5618) hydrogen bonds : bond 0.05382 / 3.77 ( 92) hydrogen bonds : angle 5.41460 / 3.73 ( 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 38 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.115 Fit side-chains REVERT: A 112 TRP cc_start: 0.5960 (t60) cc_final: 0.5577 (t60) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.1099 time to fit residues: 4.5098 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.4584 r_free = 0.4584 target = 0.203734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.172391 restraints weight = 5323.693| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 1.17 r_work: 0.4115 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3989 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3904 Z= 0.151 Angle : 0.552 6.347 5618 Z= 0.317 Chirality : 0.038 0.183 649 Planarity : 0.006 0.039 455 Dihedral : 24.442 178.658 1308 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -1.00 (0.53), residues: 256 helix: -0.25 (0.52), residues: 93 sheet: -1.82 (0.81), residues: 38 loop : -0.43 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 134 TYR 0.009 0.002 TYR A 209 PHE 0.006 0.001 PHE A 350 TRP 0.011 0.002 TRP A 112 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 3904) covalent geometry : angle 0.55243 / 0.32 ( 5618) hydrogen bonds : bond 0.05130 / 3.53 ( 92) hydrogen bonds : angle 5.07457 / 3.49 ( 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 39 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.093 Fit side-chains REVERT: A 112 TRP cc_start: 0.5948 (t60) cc_final: 0.5524 (t60) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.0993 time to fit residues: 4.2494 Evaluate side-chains 37 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 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 204 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 0.0030 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 0.4980 chunk 1 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 overall best weight: 0.2566 ------------------------------------------------------------------------------- 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 = 0.4596 r_free = 0.4596 target = 0.204942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.173640 restraints weight = 5251.942| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 1.17 r_work: 0.4131 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3904 Z= 0.140 Angle : 0.546 6.189 5618 Z= 0.312 Chirality : 0.037 0.136 649 Planarity : 0.005 0.038 455 Dihedral : 24.396 178.630 1308 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.60 % Allowed : 18.92 % 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: -0.84 (0.54), residues: 256 helix: -0.08 (0.52), residues: 93 sheet: -1.85 (0.80), residues: 38 loop : -0.33 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 134 TYR 0.014 0.002 TYR A 265 PHE 0.009 0.001 PHE A 102 TRP 0.010 0.001 TRP A 112 HIS 0.001 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 3904) covalent geometry : angle 0.54591 / 0.31 ( 5618) hydrogen bonds : bond 0.04673 / 3.17 ( 92) hydrogen bonds : angle 5.04540 / 3.44 ( 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 41 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.102 Fit side-chains REVERT: A 112 TRP cc_start: 0.5914 (t60) cc_final: 0.5513 (t60) outliers start: 8 outliers final: 8 residues processed: 37 average time/residue: 0.1120 time to fit residues: 4.9017 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 : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 204 VAL 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: 0.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.202316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.170273 restraints weight = 5206.509| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 1.21 r_work: 0.4084 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3904 Z= 0.194 Angle : 0.611 6.493 5618 Z= 0.342 Chirality : 0.041 0.144 649 Planarity : 0.006 0.050 455 Dihedral : 24.455 179.145 1308 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.05 % Allowed : 18.92 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.53), residues: 256 helix: -0.11 (0.53), residues: 93 sheet: -2.11 (0.78), residues: 38 loop : -0.44 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 134 TYR 0.011 0.002 TYR A 265 PHE 0.006 0.001 PHE A 350 TRP 0.012 0.002 TRP A 249 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 ( 3904) covalent geometry : angle 0.61060 / 0.34 ( 5618) hydrogen bonds : bond 0.05508 / 3.78 ( 92) hydrogen bonds : angle 5.15246 / 3.57 ( 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 42 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.095 Fit side-chains REVERT: A 112 TRP cc_start: 0.5926 (t60) cc_final: 0.5551 (t60) outliers start: 9 outliers final: 8 residues processed: 38 average time/residue: 0.1037 time to fit residues: 4.6480 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 : 0.093 ------------------------------------------------------------------------------- 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 204 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 316 VAL 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: 0.0270 chunk 23 optimal weight: 0.0670 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.1980 chunk 16 optimal weight: 0.0570 chunk 0 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 overall best weight: 0.0652 ------------------------------------------------------------------------------- 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 = 0.4618 r_free = 0.4618 target = 0.206760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.176001 restraints weight = 5317.770| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 1.17 r_work: 0.4158 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3904 Z= 0.128 Angle : 0.544 6.164 5618 Z= 0.310 Chirality : 0.036 0.146 649 Planarity : 0.005 0.036 455 Dihedral : 24.376 178.987 1308 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.25 % Allowed : 21.17 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.54), residues: 256 helix: -0.08 (0.51), residues: 94 sheet: -1.97 (0.78), residues: 38 loop : -0.21 (0.63), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 134 TYR 0.018 0.002 TYR A 265 PHE 0.008 0.001 PHE A 334 TRP 0.012 0.001 TRP A 318 HIS 0.001 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 3904) covalent geometry : angle 0.54402 / 0.31 ( 5618) hydrogen bonds : bond 0.04301 / 2.96 ( 92) hydrogen bonds : angle 4.87825 / 3.34 ( 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 35 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.094 Fit side-chains REVERT: A 112 TRP cc_start: 0.5861 (t60) cc_final: 0.5491 (t60) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.1150 time to fit residues: 4.5522 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 : 0.093 ------------------------------------------------------------------------------- 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 204 VAL Chi-restraints excluded: chain A residue 246 VAL 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: 0.3980 chunk 27 optimal weight: 20.0000 chunk 13 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4581 r_free = 0.4581 target = 0.203544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.172037 restraints weight = 5164.252| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 1.16 r_work: 0.4112 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3147 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= 0.169 Angle : 0.567 6.368 5618 Z= 0.320 Chirality : 0.038 0.141 649 Planarity : 0.006 0.045 455 Dihedral : 24.378 179.655 1308 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.80 % Allowed : 22.07 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.54), residues: 256 helix: -0.19 (0.51), residues: 95 sheet: -2.06 (0.79), residues: 38 loop : -0.20 (0.63), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 134 TYR 0.012 0.002 TYR A 265 PHE 0.005 0.001 PHE A 102 TRP 0.013 0.002 TRP A 249 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 3904) covalent geometry : angle 0.56710 / 0.32 ( 5618) hydrogen bonds : bond 0.05021 / 3.44 ( 92) hydrogen bonds : angle 4.95692 / 3.40 ( 236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1515.67 seconds wall clock time: 26 minutes 33.31 seconds (1593.31 seconds total)