Starting phenix.real_space_refine on Wed Mar 5 14:34:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usb_26731/03_2025/7usb_26731.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usb_26731/03_2025/7usb_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_26731/03_2025/7usb_26731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usb_26731/03_2025/7usb_26731.map" model { file = "/net/cci-nas-00/data/ceres_data/7usb_26731/03_2025/7usb_26731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usb_26731/03_2025/7usb_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-5624/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: 4.44, per 1000 atoms: 2.67 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 203.2 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: 0.44 Time building geometry restraints manager: 0.58 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: 5.470 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.950 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.230 ------------------------------------------------------------------------------- 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 : 0.169 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.1033 time to fit residues: 4.3690 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 : 0.186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.152993 restraints weight = 2012.404| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.41 r_work: 0.3637 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.189 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1575 time to fit residues: 3.8964 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 : 0.182 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 2 optimal weight: 0.0050 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 overall best weight: 0.2394 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.192685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163546 restraints weight = 1926.558| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.42 r_work: 0.3578 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1705 Z= 0.251 Angle : 0.582 4.812 2337 Z= 0.314 Chirality : 0.049 0.251 276 Planarity : 0.004 0.030 289 Dihedral : 5.219 23.852 330 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 7.64 % Favored : 90.97 % 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: -0.71 (0.54), residues: 201 helix: 1.16 (1.32), residues: 13 sheet: 0.59 (0.56), residues: 75 loop : -1.48 (0.52), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 88 HIS 0.002 0.001 HIS A 32 PHE 0.009 0.002 PHE A 180 TYR 0.008 0.001 TYR A 112 ARG 0.001 0.000 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 23 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.169 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.1297 time to fit residues: 3.3011 Evaluate side-chains 19 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 17 optimal weight: 0.0770 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 10 optimal weight: 0.0670 chunk 18 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.0040 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 5 optimal weight: 0.4980 overall best weight: 0.0646 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.188483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158282 restraints weight = 1932.828| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.49 r_work: 0.3629 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 1705 Z= 0.157 Angle : 0.495 4.903 2337 Z= 0.270 Chirality : 0.046 0.229 276 Planarity : 0.003 0.029 289 Dihedral : 4.741 23.418 330 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -0.56 (0.56), residues: 201 helix: 1.18 (1.31), residues: 13 sheet: 0.71 (0.59), residues: 74 loop : -1.37 (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 0.022 0.001 PHE A 159 TYR 0.005 0.001 TYR A 43 ARG 0.001 0.000 ARG A 154 *********************** 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 20 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.192 Fit side-chains REVERT: A 173 MET cc_start: 0.6755 (ptt) cc_final: 0.6549 (pmm) outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.1197 time to fit residues: 2.7233 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 : 0.195 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 11 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 14 optimal weight: 0.0970 chunk 1 optimal weight: 0.0870 overall best weight: 0.1232 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.186639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156130 restraints weight = 1941.489| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.52 r_work: 0.3597 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1705 Z= 0.178 Angle : 0.501 4.910 2337 Z= 0.268 Chirality : 0.046 0.228 276 Planarity : 0.003 0.026 289 Dihedral : 4.660 23.077 330 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 : 10.42 % Favored : 88.19 % 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: -0.59 (0.57), residues: 201 helix: 1.27 (1.30), residues: 13 sheet: 0.58 (0.59), residues: 74 loop : -1.32 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.001 0.000 HIS A 104 PHE 0.014 0.001 PHE A 159 TYR 0.006 0.001 TYR A 112 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 21 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.177 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.1371 time to fit residues: 3.1556 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 : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.0980 chunk 0 optimal weight: 0.1980 overall best weight: 0.1034 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.146870 restraints weight = 1966.283| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.50 r_work: 0.3585 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1705 Z= 0.155 Angle : 0.475 4.855 2337 Z= 0.256 Chirality : 0.046 0.223 276 Planarity : 0.003 0.026 289 Dihedral : 4.532 21.839 330 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.78 % Allowed : 11.11 % Favored : 86.11 % 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: -0.63 (0.58), residues: 201 helix: 1.33 (1.31), residues: 13 sheet: 0.49 (0.60), residues: 74 loop : -1.30 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 88 HIS 0.001 0.000 HIS A 104 PHE 0.017 0.001 PHE A 159 TYR 0.004 0.001 TYR A 43 ARG 0.001 0.000 ARG A 154 *********************** 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 23 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.184 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 20 average time/residue: 0.1381 time to fit residues: 3.3677 Evaluate side-chains 20 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.169201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139148 restraints weight = 1991.610| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.49 r_work: 0.3692 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 1705 Z= 0.395 Angle : 0.656 6.521 2337 Z= 0.338 Chirality : 0.053 0.265 276 Planarity : 0.004 0.042 289 Dihedral : 5.771 23.458 330 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % 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: -1.09 (0.57), residues: 201 helix: 0.87 (1.30), residues: 13 sheet: 0.20 (0.61), residues: 73 loop : -1.61 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.002 0.001 HIS A 32 PHE 0.010 0.002 PHE A 59 TYR 0.008 0.002 TYR A 58 ARG 0.002 0.000 ARG A 46 *********************** 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 22 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.7581 (pmm) cc_final: 0.7235 (ptt) outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.1399 time to fit residues: 3.5473 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 : 0.268 ------------------------------------------------------------------------------- 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 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 6 optimal weight: 0.0870 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147446 restraints weight = 1958.605| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.46 r_work: 0.3711 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1705 Z= 0.285 Angle : 0.566 4.597 2337 Z= 0.297 Chirality : 0.050 0.258 276 Planarity : 0.003 0.032 289 Dihedral : 5.739 26.198 330 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % 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: -1.18 (0.58), residues: 201 helix: 0.94 (1.31), residues: 13 sheet: 0.06 (0.62), residues: 73 loop : -1.62 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.001 0.001 HIS A 32 PHE 0.015 0.002 PHE A 159 TYR 0.004 0.001 TYR A 112 ARG 0.001 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 24 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.7518 (pmm) cc_final: 0.7297 (ptt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1267 time to fit residues: 3.5310 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 : 0.176 ------------------------------------------------------------------------------- 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 4 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 18 optimal weight: 0.0870 chunk 3 optimal weight: 0.0870 overall best weight: 0.1132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143173 restraints weight = 1984.444| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.63 r_work: 0.3726 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 1705 Z= 0.224 Angle : 0.665 14.620 2337 Z= 0.346 Chirality : 0.047 0.236 276 Planarity : 0.003 0.029 289 Dihedral : 5.597 23.949 330 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.78 % Allowed : 12.50 % 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: -1.27 (0.57), residues: 201 helix: 1.13 (1.33), residues: 13 sheet: -0.10 (0.61), residues: 76 loop : -1.67 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.001 0.000 HIS A 32 PHE 0.017 0.001 PHE A 159 TYR 0.006 0.001 TYR A 77 ARG 0.000 0.000 ARG A 46 *********************** 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: 4 poor density : 22 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.7501 (pmm) cc_final: 0.7295 (ptt) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.1284 time to fit residues: 3.7744 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 : 0.237 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.0020 chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 0.0970 chunk 18 optimal weight: 0.3980 chunk 1 optimal weight: 0.0870 chunk 16 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 overall best weight: 0.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146162 restraints weight = 2041.804| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.58 r_work: 0.3560 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 1705 Z= 0.183 Angle : 0.571 8.702 2337 Z= 0.302 Chirality : 0.046 0.218 276 Planarity : 0.003 0.024 289 Dihedral : 5.310 29.851 330 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.85 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: -1.10 (0.57), residues: 201 helix: 1.37 (1.33), residues: 13 sheet: 0.05 (0.60), residues: 76 loop : -1.61 (0.54), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.001 0.000 HIS A 104 PHE 0.007 0.001 PHE A 159 TYR 0.012 0.001 TYR A 257 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 24 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.7486 (pmm) cc_final: 0.7271 (ptt) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1244 time to fit residues: 3.3298 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 : 0.171 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 18 optimal weight: 0.0770 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144471 restraints weight = 2034.434| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.57 r_work: 0.3538 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 1705 Z= 0.224 Angle : 0.570 8.214 2337 Z= 0.301 Chirality : 0.047 0.226 276 Planarity : 0.003 0.026 289 Dihedral : 5.159 24.016 330 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.53 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: -1.13 (0.57), residues: 201 helix: -0.08 (1.10), residues: 19 sheet: 0.02 (0.60), residues: 76 loop : -1.48 (0.56), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.001 0.000 HIS A 104 PHE 0.004 0.001 PHE A 180 TYR 0.009 0.001 TYR A 77 ARG 0.000 0.000 ARG A 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1820.58 seconds wall clock time: 31 minutes 55.51 seconds (1915.51 seconds total)