Starting phenix.real_space_refine on Fri Dec 27 04:16:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usb_26731/12_2024/7usb_26731.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usb_26731/12_2024/7usb_26731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7usb_26731/12_2024/7usb_26731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usb_26731/12_2024/7usb_26731.map" model { file = "/net/cci-nas-00/data/ceres_data/7usb_26731/12_2024/7usb_26731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usb_26731/12_2024/7usb_26731.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1078 2.51 5 N 279 2.21 5 O 292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 1661 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 5 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.90, per 1000 atoms: 2.95 Number of scatterers: 1661 At special positions: 0 Unit cell: (57.324, 67.44, 57.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 292 8.00 N 279 7.00 C 1078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 170 " distance=2.04 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 254 " distance=2.13 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A5401 " - " ASN A 242 " " NAG A5402 " - " ASN A 26 " " NAG A5403 " - " ASN A 42 " " NAG B 1 " - " ASN A 249 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 273.5 milliseconds 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 404 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 4 sheets defined 13.6% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 254 through 258 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 80 removed outlier: 7.297A pdb=" N PHE A 202 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS A 110 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR A 204 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 130 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 155 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 132 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS A 153 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 196 64 hydrogen bonds defined for protein. 150 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 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: 1.20 - 1.33: 390 1.33 - 1.46: 470 1.46 - 1.58: 830 1.58 - 1.71: 1 1.71 - 1.84: 14 Bond restraints: 1705 Sorted by residual: bond pdb=" CB LEU A 207 " pdb=" CG LEU A 207 " ideal model delta sigma weight residual 1.530 1.602 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CA PRO A 48 " pdb=" C PRO A 48 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.23e+01 bond pdb=" C5 NAG A5401 " pdb=" O5 NAG A5401 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C5 NAG A5402 " pdb=" O5 NAG A5402 " ideal model delta sigma weight residual 1.413 1.475 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" NE ARG A 194 " pdb=" CZ ARG A 194 " ideal model delta sigma weight residual 1.326 1.358 -0.032 1.10e-02 8.26e+03 8.45e+00 ... (remaining 1700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 2285 4.50 - 8.99: 46 8.99 - 13.49: 2 13.49 - 17.98: 2 17.98 - 22.48: 2 Bond angle restraints: 2337 Sorted by residual: angle pdb=" CD1 LEU A 41 " pdb=" CG LEU A 41 " pdb=" CD2 LEU A 41 " ideal model delta sigma weight residual 110.80 133.28 -22.48 2.20e+00 2.07e-01 1.04e+02 angle pdb=" C LEU A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta sigma weight residual 119.66 127.07 -7.41 7.30e-01 1.88e+00 1.03e+02 angle pdb=" CG1 VAL A 185 " pdb=" CB VAL A 185 " pdb=" CG2 VAL A 185 " ideal model delta sigma weight residual 110.80 131.09 -20.29 2.20e+00 2.07e-01 8.50e+01 angle pdb=" C PRO A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.56 127.28 -7.72 1.01e+00 9.80e-01 5.84e+01 angle pdb=" C PRO A 137 " pdb=" N PRO A 138 " pdb=" CA PRO A 138 " ideal model delta sigma weight residual 120.03 126.02 -5.99 9.90e-01 1.02e+00 3.67e+01 ... (remaining 2332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 992 17.81 - 35.63: 39 35.63 - 53.44: 7 53.44 - 71.25: 6 71.25 - 89.07: 1 Dihedral angle restraints: 1045 sinusoidal: 422 harmonic: 623 Sorted by residual: dihedral pdb=" CB CYS A 21 " pdb=" SG CYS A 21 " pdb=" SG CYS A 68 " pdb=" CB CYS A 68 " ideal model delta sinusoidal sigma weight residual 93.00 162.97 -69.97 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS A 250 " pdb=" SG CYS A 250 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 153.68 -60.68 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 -142.30 56.30 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 1042 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.109: 226 0.109 - 0.216: 31 0.216 - 0.323: 11 0.323 - 0.430: 6 0.430 - 0.537: 2 Chirality restraints: 276 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.73e+01 chirality pdb=" CG LEU A 41 " pdb=" CB LEU A 41 " pdb=" CD1 LEU A 41 " pdb=" CD2 LEU A 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CB VAL A 185 " pdb=" CA VAL A 185 " pdb=" CG1 VAL A 185 " pdb=" CG2 VAL A 185 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 273 not shown) Planarity restraints: 293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A5403 " -0.211 2.00e-02 2.50e+03 1.79e-01 4.01e+02 pdb=" C7 NAG A5403 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG A5403 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG A5403 " 0.294 2.00e-02 2.50e+03 pdb=" O7 NAG A5403 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.103 2.00e-02 2.50e+03 8.70e-02 9.46e+01 pdb=" C7 NAG B 2 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.138 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 133 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C CYS A 133 " 0.071 2.00e-02 2.50e+03 pdb=" O CYS A 133 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS A 134 " -0.024 2.00e-02 2.50e+03 ... (remaining 290 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 931 3.05 - 3.51: 1400 3.51 - 3.98: 2544 3.98 - 4.44: 2901 4.44 - 4.90: 4618 Nonbonded interactions: 12394 Sorted by model distance: nonbonded pdb=" N GLY A 243 " pdb=" N THR A 244 " model vdw 2.590 2.560 nonbonded pdb=" N PHE A 202 " pdb=" O PHE A 202 " model vdw 2.614 2.496 nonbonded pdb=" O LYS A 110 " pdb=" CD PRO A 111 " model vdw 2.626 2.752 nonbonded pdb=" OD1 ASP A 89 " pdb=" N TYR A 90 " model vdw 2.634 3.120 nonbonded pdb=" N GLN A 167 " pdb=" O GLN A 167 " model vdw 2.647 2.496 ... (remaining 12389 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: 10.590 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 13.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.013 0.072 1705 Z= 0.838 Angle : 1.720 22.477 2337 Z= 1.049 Chirality : 0.110 0.537 276 Planarity : 0.013 0.179 289 Dihedral : 10.319 89.066 626 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.39 % Allowed : 1.39 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.53), residues: 201 helix: -1.80 (0.97), residues: 18 sheet: 1.28 (0.53), residues: 75 loop : -1.01 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP A 88 HIS 0.003 0.001 HIS A 189 PHE 0.009 0.003 PHE A 227 TYR 0.023 0.005 TYR A 90 ARG 0.001 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.186 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.1070 time to fit residues: 4.5335 Evaluate side-chains 18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 0.3980 chunk 15 optimal weight: 0.0980 chunk 8 optimal weight: 0.1980 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 overall best weight: 0.1338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1705 Z= 0.219 Angle : 0.632 4.830 2337 Z= 0.351 Chirality : 0.049 0.241 276 Planarity : 0.004 0.032 289 Dihedral : 5.452 23.045 331 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.39 % Allowed : 5.56 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.54), residues: 201 helix: 1.72 (1.41), residues: 12 sheet: 1.02 (0.56), residues: 75 loop : -1.15 (0.50), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 88 HIS 0.002 0.001 HIS A 189 PHE 0.011 0.001 PHE A 24 TYR 0.008 0.001 TYR A 175 ARG 0.002 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.155 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1539 time to fit residues: 3.7867 Evaluate side-chains 18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.0060 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1705 Z= 0.315 Angle : 0.639 5.446 2337 Z= 0.340 Chirality : 0.051 0.262 276 Planarity : 0.004 0.035 289 Dihedral : 5.654 24.374 330 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.08 % Allowed : 5.56 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.56), residues: 201 helix: 1.13 (1.35), residues: 13 sheet: 0.53 (0.59), residues: 75 loop : -1.64 (0.52), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 88 HIS 0.001 0.000 HIS A 32 PHE 0.014 0.002 PHE A 180 TYR 0.010 0.002 TYR A 112 ARG 0.002 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.184 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1308 time to fit residues: 3.6551 Evaluate side-chains 21 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 14 optimal weight: 0.0980 chunk 10 optimal weight: 0.1980 chunk 18 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 overall best weight: 0.1154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 1705 Z= 0.173 Angle : 0.527 4.746 2337 Z= 0.282 Chirality : 0.047 0.240 276 Planarity : 0.003 0.030 289 Dihedral : 5.078 24.133 330 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 9.72 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.56), residues: 201 helix: 1.04 (1.32), residues: 13 sheet: 0.43 (0.59), residues: 74 loop : -1.50 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.001 0.000 HIS A 104 PHE 0.019 0.001 PHE A 159 TYR 0.005 0.001 TYR A 112 ARG 0.001 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.182 Fit side-chains REVERT: A 173 MET cc_start: 0.6784 (pmm) cc_final: 0.6449 (ptt) outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.1523 time to fit residues: 3.6349 Evaluate side-chains 20 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.0980 chunk 4 optimal weight: 0.1980 chunk 11 optimal weight: 0.0270 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1705 Z= 0.253 Angle : 0.567 5.163 2337 Z= 0.298 Chirality : 0.049 0.249 276 Planarity : 0.004 0.031 289 Dihedral : 5.310 25.175 330 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.78 % Allowed : 11.81 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.57), residues: 201 helix: 1.05 (1.31), residues: 13 sheet: 0.32 (0.61), residues: 73 loop : -1.59 (0.54), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.001 0.001 HIS A 189 PHE 0.011 0.002 PHE A 159 TYR 0.006 0.001 TYR A 58 ARG 0.001 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.165 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.1135 time to fit residues: 2.9223 Evaluate side-chains 21 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1705 Z= 0.297 Angle : 0.578 4.748 2337 Z= 0.306 Chirality : 0.050 0.259 276 Planarity : 0.004 0.031 289 Dihedral : 5.705 24.907 330 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.58), residues: 201 helix: 0.89 (1.32), residues: 13 sheet: 0.16 (0.62), residues: 73 loop : -1.68 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.002 0.001 HIS A 32 PHE 0.007 0.001 PHE A 197 TYR 0.005 0.001 TYR A 112 ARG 0.001 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.183 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1351 time to fit residues: 3.7534 Evaluate side-chains 23 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 0.3980 chunk 1 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 18 optimal weight: 0.1980 chunk 19 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 8 optimal weight: 0.1980 chunk 14 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1705 Z= 0.215 Angle : 0.530 4.709 2337 Z= 0.282 Chirality : 0.048 0.245 276 Planarity : 0.003 0.031 289 Dihedral : 5.511 25.143 330 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 11.11 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.58), residues: 201 helix: 0.94 (1.33), residues: 13 sheet: 0.10 (0.61), residues: 73 loop : -1.61 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.003 0.001 HIS A 189 PHE 0.004 0.001 PHE A 227 TYR 0.004 0.001 TYR A 43 ARG 0.001 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.194 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1291 time to fit residues: 3.6041 Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 1705 Z= 0.491 Angle : 0.804 15.327 2337 Z= 0.409 Chirality : 0.054 0.282 276 Planarity : 0.005 0.043 289 Dihedral : 6.623 27.069 330 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.47 % Allowed : 11.81 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.56), residues: 201 helix: 0.44 (1.32), residues: 13 sheet: -0.15 (0.62), residues: 72 loop : -2.12 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 179 HIS 0.002 0.001 HIS A 32 PHE 0.010 0.002 PHE A 197 TYR 0.006 0.002 TYR A 58 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.189 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.1436 time to fit residues: 4.5403 Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.2980 chunk 4 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 0.0980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.1980 chunk 11 optimal weight: 0.4980 overall best weight: 0.1578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 1705 Z= 0.244 Angle : 0.632 11.322 2337 Z= 0.333 Chirality : 0.048 0.242 276 Planarity : 0.003 0.032 289 Dihedral : 6.257 28.512 330 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.57), residues: 201 helix: 0.68 (1.33), residues: 13 sheet: -0.08 (0.61), residues: 72 loop : -1.97 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 88 HIS 0.002 0.001 HIS A 189 PHE 0.003 0.001 PHE A 227 TYR 0.007 0.001 TYR A 77 ARG 0.001 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.180 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1523 time to fit residues: 4.2672 Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.0040 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 chunk 20 optimal weight: 0.0670 chunk 3 optimal weight: 0.0980 chunk 2 optimal weight: 0.0670 chunk 4 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 overall best weight: 0.0646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 1705 Z= 0.185 Angle : 0.554 5.870 2337 Z= 0.300 Chirality : 0.046 0.219 276 Planarity : 0.003 0.024 289 Dihedral : 5.476 28.654 330 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 13.89 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.58), residues: 201 helix: 0.81 (1.35), residues: 13 sheet: -0.23 (0.60), residues: 77 loop : -1.73 (0.56), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.003 0.001 HIS A 189 PHE 0.003 0.001 PHE A 227 TYR 0.007 0.001 TYR A 77 ARG 0.001 0.000 ARG A 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.200 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.1551 time to fit residues: 4.5352 Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 0.0570 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.0670 chunk 13 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 overall best weight: 0.0674 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.178870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152106 restraints weight = 1933.160| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.21 r_work: 0.3590 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1705 Z= 0.174 Angle : 0.551 6.993 2337 Z= 0.296 Chirality : 0.046 0.220 276 Planarity : 0.003 0.022 289 Dihedral : 4.982 23.575 330 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 14.58 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.57), residues: 201 helix: -0.08 (1.11), residues: 19 sheet: -0.15 (0.60), residues: 79 loop : -1.57 (0.57), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 149 HIS 0.001 0.000 HIS A 189 PHE 0.003 0.001 PHE A 227 TYR 0.010 0.001 TYR A 257 ARG 0.001 0.000 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1367.79 seconds wall clock time: 26 minutes 11.92 seconds (1571.92 seconds total)