Starting phenix.real_space_refine on Fri Oct 10 11:17:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrw_37792/10_2025/8wrw_37792.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrw_37792/10_2025/8wrw_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_37792/10_2025/8wrw_37792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrw_37792/10_2025/8wrw_37792.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrw_37792/10_2025/8wrw_37792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrw_37792/10_2025/8wrw_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-2.0-5842/lib/python3.9/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: 1.46, per 1000 atoms: 0.40 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: 0.44 Conformation dependent library (CDL) restraints added in 91.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.59 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: 0.71 Time building geometry restraints manager: 0.56 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=" 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=" N ARG A 154 " pdb=" CA ARG A 154 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.21e-02 6.83e+03 3.73e+00 bond pdb=" C ARG A 310 " pdb=" O ARG A 310 " ideal model delta sigma weight residual 1.237 1.217 0.019 1.17e-02 7.31e+03 2.71e+00 bond pdb=" C HIS A 214 " pdb=" N PRO A 215 " ideal model delta sigma weight residual 1.341 1.366 -0.025 1.60e-02 3.91e+03 2.42e+00 bond pdb=" C GLU A 148 " pdb=" O GLU A 148 " ideal model delta sigma weight residual 1.237 1.219 0.018 1.17e-02 7.31e+03 2.41e+00 ... (remaining 3899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5429 1.99 - 3.98: 163 3.98 - 5.96: 13 5.96 - 7.95: 9 7.95 - 9.94: 4 Bond angle restraints: 5618 Sorted by residual: angle pdb=" N LYS A 153 " pdb=" CA LYS A 153 " pdb=" C LYS A 153 " ideal model delta sigma weight residual 111.28 106.92 4.36 1.09e+00 8.42e-01 1.60e+01 angle pdb=" N ASP A 101 " pdb=" CA ASP A 101 " pdb=" C ASP A 101 " ideal model delta sigma weight residual 107.37 99.14 8.23 2.07e+00 2.33e-01 1.58e+01 angle pdb=" C ARG A 154 " pdb=" N ARG A 155 " pdb=" CA ARG A 155 " ideal model delta sigma weight residual 121.58 114.02 7.56 1.95e+00 2.63e-01 1.50e+01 angle pdb=" N GLY A 337 " pdb=" CA GLY A 337 " pdb=" C GLY A 337 " ideal model delta sigma weight residual 113.24 108.27 4.97 1.31e+00 5.83e-01 1.44e+01 angle pdb=" N VAL A 204 " pdb=" CA VAL A 204 " pdb=" CB VAL A 204 " ideal model delta sigma weight residual 112.21 108.17 4.04 1.10e+00 8.26e-01 1.35e+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: 517 0.051 - 0.102: 101 0.102 - 0.153: 24 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: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.990 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.020 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:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 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 0.041 3904 Z= 0.254 Angle : 0.807 9.937 5618 Z= 0.455 Chirality : 0.046 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 aren 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 covalent geometry : bond 0.00459 ( 3904) covalent geometry : angle 0.80700 ( 5618) hydrogen bonds : bond 0.27591 ( 92) hydrogen bonds : angle 10.91401 ( 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 : 0.106 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 34 average time/residue: 0.1070 time to fit residues: 4.2604 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 : 0.101 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.203608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.170998 restraints weight = 5056.134| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 1.24 r_work: 0.4097 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3974 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3904 Z= 0.195 Angle : 0.674 7.454 5618 Z= 0.344 Chirality : 0.040 0.161 649 Planarity : 0.007 0.065 455 Dihedral : 24.615 179.910 1310 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.70 % Allowed : 6.31 % Favored : 90.99 % 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 aren not related in a simple way. whole: -1.22 (0.54), residues: 256 helix: -0.74 (0.51), residues: 99 sheet: -2.14 (0.86), residues: 32 loop : -0.29 (0.62), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.011 0.002 TYR A 89 PHE 0.012 0.002 PHE A 335 TRP 0.013 0.002 TRP A 75 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 3904) covalent geometry : angle 0.67429 ( 5618) hydrogen bonds : bond 0.06792 ( 92) hydrogen bonds : angle 6.30276 ( 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 : 0.101 Fit side-chains revert: symmetry clash REVERT: A 112 TRP cc_start: 0.5815 (t60) cc_final: 0.5552 (t60) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.0902 time to fit residues: 3.6514 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 : 0.101 ------------------------------------------------------------------------------- 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: 0.0070 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 11 optimal weight: 0.0070 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.204440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.171224 restraints weight = 5097.174| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.29 r_work: 0.4098 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3904 Z= 0.172 Angle : 0.622 6.410 5618 Z= 0.321 Chirality : 0.038 0.138 649 Planarity : 0.007 0.055 455 Dihedral : 24.428 179.196 1309 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.25 % Allowed : 13.06 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.55), residues: 256 helix: -0.23 (0.55), residues: 91 sheet: -1.97 (0.81), residues: 38 loop : -0.41 (0.61), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 134 TYR 0.009 0.002 TYR A 209 PHE 0.009 0.002 PHE A 335 TRP 0.009 0.002 TRP A 318 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3904) covalent geometry : angle 0.62221 ( 5618) hydrogen bonds : bond 0.05421 ( 92) hydrogen bonds : angle 5.42359 ( 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 40 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 112 TRP cc_start: 0.5826 (t60) cc_final: 0.5497 (t60) REVERT: A 308 ASP cc_start: 0.6858 (t0) cc_final: 0.6612 (t70) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.0982 time to fit residues: 4.2544 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 : 0.103 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 13 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.0470 chunk 20 optimal weight: 0.2980 chunk 23 optimal weight: 0.0170 chunk 28 optimal weight: 0.9990 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.207366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.176497 restraints weight = 5147.818| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 1.17 r_work: 0.4165 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3904 Z= 0.128 Angle : 0.555 6.275 5618 Z= 0.286 Chirality : 0.035 0.134 649 Planarity : 0.006 0.047 455 Dihedral : 24.330 179.867 1308 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.35 % Allowed : 17.12 % Favored : 81.53 % 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 aren not related in a simple way. whole: -0.91 (0.54), residues: 256 helix: -0.19 (0.53), residues: 92 sheet: -1.58 (0.83), residues: 38 loop : -0.43 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.010 0.002 TYR A 245 PHE 0.011 0.001 PHE A 335 TRP 0.008 0.001 TRP A 318 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3904) covalent geometry : angle 0.55522 ( 5618) hydrogen bonds : bond 0.04247 ( 92) hydrogen bonds : angle 4.87666 ( 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 32 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 137 PHE cc_start: 0.7456 (m-80) cc_final: 0.6878 (m-80) REVERT: A 308 ASP cc_start: 0.6801 (t0) cc_final: 0.6567 (t70) outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 0.0992 time to fit residues: 3.7365 Evaluate side-chains 31 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 6 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.202692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.170842 restraints weight = 5152.595| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 1.19 r_work: 0.4093 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3904 Z= 0.187 Angle : 0.623 6.529 5618 Z= 0.317 Chirality : 0.038 0.143 649 Planarity : 0.006 0.045 455 Dihedral : 24.395 179.117 1308 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.60 % Allowed : 17.12 % 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 aren not related in a simple way. whole: -0.97 (0.54), residues: 256 helix: -0.22 (0.54), residues: 93 sheet: -1.79 (0.83), residues: 38 loop : -0.44 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.010 0.002 TYR A 209 PHE 0.010 0.002 PHE A 335 TRP 0.023 0.002 TRP A 112 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 3904) covalent geometry : angle 0.62322 ( 5618) hydrogen bonds : bond 0.05271 ( 92) hydrogen bonds : angle 5.07216 ( 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 42 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.119 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 0.1084 time to fit residues: 4.9055 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 : 0.087 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.0670 chunk 11 optimal weight: 0.0570 chunk 17 optimal weight: 0.9990 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.205502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.174227 restraints weight = 5221.739| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 1.20 r_work: 0.4138 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.3038 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= 0.136 Angle : 0.563 6.214 5618 Z= 0.288 Chirality : 0.035 0.137 649 Planarity : 0.005 0.041 455 Dihedral : 24.235 179.111 1308 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 aren not related in a simple way. whole: -0.95 (0.54), residues: 256 helix: -0.25 (0.52), residues: 94 sheet: -1.54 (0.81), residues: 38 loop : -0.47 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 134 TYR 0.009 0.001 TYR A 201 PHE 0.010 0.001 PHE A 335 TRP 0.016 0.001 TRP A 112 HIS 0.001 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3904) covalent geometry : angle 0.56252 ( 5618) hydrogen bonds : bond 0.04372 ( 92) hydrogen bonds : angle 4.72936 ( 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 35 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.108 Fit side-chains REVERT: A 112 TRP cc_start: 0.5865 (t60) cc_final: 0.5459 (t60) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.0877 time to fit residues: 3.6173 Evaluate side-chains 34 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.083 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 19 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.202726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.170950 restraints weight = 5288.091| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.22 r_work: 0.4096 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3968 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3904 Z= 0.180 Angle : 0.610 6.354 5618 Z= 0.310 Chirality : 0.038 0.142 649 Planarity : 0.006 0.043 455 Dihedral : 24.275 178.273 1308 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.60 % Allowed : 17.57 % 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 aren not related in a simple way. whole: -1.09 (0.53), residues: 256 helix: -0.41 (0.51), residues: 97 sheet: -1.92 (0.77), residues: 38 loop : -0.37 (0.61), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 134 TYR 0.027 0.002 TYR A 140 PHE 0.009 0.001 PHE A 335 TRP 0.015 0.002 TRP A 112 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3904) covalent geometry : angle 0.60962 ( 5618) hydrogen bonds : bond 0.04958 ( 92) hydrogen bonds : angle 4.89694 ( 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 : 0.104 Fit side-chains REVERT: A 112 TRP cc_start: 0.5853 (t60) cc_final: 0.5470 (t60) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.1046 time to fit residues: 4.2989 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 : 0.063 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.201825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.169264 restraints weight = 5156.725| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 1.23 r_work: 0.4071 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3948 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3904 Z= 0.220 Angle : 0.670 7.292 5618 Z= 0.341 Chirality : 0.041 0.149 649 Planarity : 0.006 0.043 455 Dihedral : 24.424 179.999 1308 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.60 % Allowed : 17.12 % 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 aren not related in a simple way. whole: -1.26 (0.53), residues: 256 helix: -0.45 (0.51), residues: 96 sheet: -2.12 (0.80), residues: 38 loop : -0.54 (0.61), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 134 TYR 0.026 0.003 TYR A 140 PHE 0.012 0.002 PHE A 335 TRP 0.015 0.002 TRP A 112 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 3904) covalent geometry : angle 0.66996 ( 5618) hydrogen bonds : bond 0.05565 ( 92) hydrogen bonds : angle 5.13673 ( 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 39 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.068 Fit side-chains REVERT: A 112 TRP cc_start: 0.5848 (t60) cc_final: 0.5440 (t60) outliers start: 8 outliers final: 6 residues processed: 36 average time/residue: 0.1207 time to fit residues: 4.9970 Evaluate side-chains 35 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.072 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.0000 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.203095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170254 restraints weight = 5168.255| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.28 r_work: 0.4082 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3904 Z= 0.193 Angle : 0.645 7.528 5618 Z= 0.328 Chirality : 0.039 0.144 649 Planarity : 0.006 0.039 455 Dihedral : 24.372 179.996 1308 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.15 % Allowed : 17.57 % 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 aren not related in a simple way. whole: -1.12 (0.53), residues: 256 helix: -0.32 (0.52), residues: 94 sheet: -1.99 (0.82), residues: 38 loop : -0.49 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 134 TYR 0.022 0.002 TYR A 140 PHE 0.008 0.002 PHE A 102 TRP 0.015 0.002 TRP A 112 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 3904) covalent geometry : angle 0.64477 ( 5618) hydrogen bonds : bond 0.05091 ( 92) hydrogen bonds : angle 5.04991 ( 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 37 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.141 Fit side-chains REVERT: A 112 TRP cc_start: 0.5869 (t60) cc_final: 0.5445 (t60) outliers start: 7 outliers final: 7 residues processed: 34 average time/residue: 0.1225 time to fit residues: 4.8106 Evaluate side-chains 36 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TRP 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: 0.0050 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 0.0770 chunk 0 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.2952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.204370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.172962 restraints weight = 5264.662| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 1.21 r_work: 0.4116 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3990 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3904 Z= 0.152 Angle : 0.591 6.315 5618 Z= 0.302 Chirality : 0.037 0.164 649 Planarity : 0.006 0.038 455 Dihedral : 24.239 179.301 1308 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.25 % Allowed : 18.47 % 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 aren not related in a simple way. whole: -0.85 (0.54), residues: 256 helix: -0.12 (0.52), residues: 95 sheet: -1.79 (0.82), residues: 38 loop : -0.34 (0.62), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 134 TYR 0.019 0.002 TYR A 140 PHE 0.011 0.002 PHE A 137 TRP 0.015 0.002 TRP A 112 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3904) covalent geometry : angle 0.59055 ( 5618) hydrogen bonds : bond 0.04495 ( 92) hydrogen bonds : angle 4.81441 ( 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 33 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.099 Fit side-chains REVERT: A 112 TRP cc_start: 0.5792 (t60) cc_final: 0.5356 (t60) outliers start: 5 outliers final: 5 residues processed: 31 average time/residue: 0.0816 time to fit residues: 3.0829 Evaluate side-chains 33 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.067 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 22 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 19 optimal weight: 0.0570 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.205478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.173880 restraints weight = 5160.406| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 1.19 r_work: 0.4129 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3904 Z= 0.137 Angle : 0.563 5.954 5618 Z= 0.288 Chirality : 0.035 0.136 649 Planarity : 0.005 0.040 455 Dihedral : 24.103 178.722 1308 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.80 % Allowed : 19.82 % 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 aren not related in a simple way. whole: -0.77 (0.55), residues: 256 helix: -0.05 (0.51), residues: 97 sheet: -1.91 (0.82), residues: 39 loop : -0.20 (0.64), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 134 TYR 0.018 0.002 TYR A 140 PHE 0.007 0.001 PHE A 137 TRP 0.014 0.002 TRP A 112 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3904) covalent geometry : angle 0.56277 ( 5618) hydrogen bonds : bond 0.04308 ( 92) hydrogen bonds : angle 4.59198 ( 236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.59 seconds wall clock time: 25 minutes 59.14 seconds (1559.14 seconds total)