Starting phenix.real_space_refine on Fri Oct 10 10:30:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p7l_17536/10_2025/8p7l_17536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p7l_17536/10_2025/8p7l_17536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p7l_17536/10_2025/8p7l_17536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p7l_17536/10_2025/8p7l_17536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p7l_17536/10_2025/8p7l_17536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p7l_17536/10_2025/8p7l_17536.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 1635 2.51 5 N 429 2.21 5 O 492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2568 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 194 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain breaks: 1 Chain: "J" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2300 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 270} Chain breaks: 2 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'WD9': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Time building chain proxies: 0.98, per 1000 atoms: 0.38 Number of scatterers: 2568 At special positions: 0 Unit cell: (59.85, 77.805, 68.4, 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 492 8.00 N 429 7.00 C 1635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 63.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 586 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 44.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 289 through 296 removed outlier: 3.808A pdb=" N CYS H 293 " --> pdb=" O SER H 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.915A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 removed outlier: 3.938A pdb=" N LEU J 222 " --> pdb=" O ASP J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 243 removed outlier: 3.592A pdb=" N LEU J 243 " --> pdb=" O MET J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.934A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 12 through 20 removed outlier: 6.612A pdb=" N LYS J 28 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHE J 17 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL J 26 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY J 19 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA J 24 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN J 36 " --> pdb=" O ASP J 31 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE J 87 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 99 hydrogen bonds defined for protein. 279 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: 0.36 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 808 1.34 - 1.46: 560 1.46 - 1.58: 1202 1.58 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 2589 Sorted by residual: bond pdb=" C9 WD9 J 401 " pdb=" N13 WD9 J 401 " ideal model delta sigma weight residual 1.326 1.463 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C7 WD9 J 401 " pdb=" O26 WD9 J 401 " ideal model delta sigma weight residual 1.322 1.407 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C5 WD9 J 401 " pdb=" N10 WD9 J 401 " ideal model delta sigma weight residual 1.379 1.298 0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" N10 WD9 J 401 " pdb=" N11 WD9 J 401 " ideal model delta sigma weight residual 1.342 1.410 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C27 WD9 J 401 " pdb=" C28 WD9 J 401 " ideal model delta sigma weight residual 1.535 1.487 0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 2584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 3430 1.99 - 3.97: 69 3.97 - 5.96: 7 5.96 - 7.95: 2 7.95 - 9.93: 1 Bond angle restraints: 3509 Sorted by residual: angle pdb=" C27 WD9 J 401 " pdb=" O26 WD9 J 401 " pdb=" C7 WD9 J 401 " ideal model delta sigma weight residual 120.40 110.47 9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N6 WD9 J 401 " pdb=" C7 WD9 J 401 " pdb=" N8 WD9 J 401 " ideal model delta sigma weight residual 127.26 119.88 7.38 3.00e+00 1.11e-01 6.06e+00 angle pdb=" C4 WD9 J 401 " pdb=" C12 WD9 J 401 " pdb=" N11 WD9 J 401 " ideal model delta sigma weight residual 114.13 107.60 6.53 3.00e+00 1.11e-01 4.74e+00 angle pdb=" CB GLU J 95 " pdb=" CG GLU J 95 " pdb=" CD GLU J 95 " ideal model delta sigma weight residual 112.60 115.94 -3.34 1.70e+00 3.46e-01 3.86e+00 angle pdb=" CA GLU J 62 " pdb=" CB GLU J 62 " pdb=" CG GLU J 62 " ideal model delta sigma weight residual 114.10 117.78 -3.68 2.00e+00 2.50e-01 3.39e+00 ... (remaining 3504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 1364 17.28 - 34.55: 145 34.55 - 51.83: 34 51.83 - 69.11: 4 69.11 - 86.38: 5 Dihedral angle restraints: 1552 sinusoidal: 645 harmonic: 907 Sorted by residual: dihedral pdb=" CB GLU J 126 " pdb=" CG GLU J 126 " pdb=" CD GLU J 126 " pdb=" OE1 GLU J 126 " ideal model delta sinusoidal sigma weight residual 0.00 86.38 -86.38 1 3.00e+01 1.11e-03 9.99e+00 dihedral pdb=" N VAL J 210 " pdb=" CA VAL J 210 " pdb=" CB VAL J 210 " pdb=" CG1 VAL J 210 " ideal model delta sinusoidal sigma weight residual 180.00 125.39 54.61 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" CG ARG J 309 " pdb=" CD ARG J 309 " pdb=" NE ARG J 309 " pdb=" CZ ARG J 309 " ideal model delta sinusoidal sigma weight residual 180.00 139.61 40.39 2 1.50e+01 4.44e-03 8.96e+00 ... (remaining 1549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 287 0.046 - 0.092: 79 0.092 - 0.138: 20 0.138 - 0.184: 0 0.184 - 0.230: 1 Chirality restraints: 387 Sorted by residual: chirality pdb=" C27 WD9 J 401 " pdb=" C28 WD9 J 401 " pdb=" C32 WD9 J 401 " pdb=" O26 WD9 J 401 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE J 255 " pdb=" N ILE J 255 " pdb=" C ILE J 255 " pdb=" CB ILE J 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE J 74 " pdb=" N ILE J 74 " pdb=" C ILE J 74 " pdb=" CB ILE J 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 384 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 279 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO H 280 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 280 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 280 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 210 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO J 211 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 211 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 211 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 71 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO J 72 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO J 72 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 72 " -0.016 5.00e-02 4.00e+02 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 402 2.76 - 3.29: 2610 3.29 - 3.83: 4575 3.83 - 4.36: 5654 4.36 - 4.90: 9241 Nonbonded interactions: 22482 Sorted by model distance: nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR J 294 " pdb=" O HOH J 501 " model vdw 2.228 3.040 nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 402 " model vdw 2.260 3.040 nonbonded pdb=" O TRP J 177 " pdb=" O HOH J 502 " model vdw 2.266 3.040 nonbonded pdb=" O HOH J 514 " pdb=" O HOH J 533 " model vdw 2.269 3.040 ... (remaining 22477 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: 1.990 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: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 4.290 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 2589 Z= 0.261 Angle : 0.675 9.932 3509 Z= 0.325 Chirality : 0.045 0.230 387 Planarity : 0.005 0.040 445 Dihedral : 15.629 86.384 966 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.95 % Favored : 96.72 % Rotamer: Outliers : 1.11 % Allowed : 18.89 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.47), residues: 305 helix: 0.13 (0.49), residues: 109 sheet: -0.93 (1.05), residues: 20 loop : -0.14 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 11 TYR 0.011 0.002 TYR J 127 PHE 0.015 0.002 PHE J 91 TRP 0.008 0.001 TRP J 132 HIS 0.003 0.001 HIS J 259 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 2589) covalent geometry : angle 0.67525 ( 3509) hydrogen bonds : bond 0.10073 ( 99) hydrogen bonds : angle 7.07450 ( 279) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.112 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.5366 time to fit residues: 28.0031 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 242 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.187025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.167390 restraints weight = 2658.574| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.31 r_work: 0.3982 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2589 Z= 0.123 Angle : 0.539 4.115 3509 Z= 0.276 Chirality : 0.043 0.127 387 Planarity : 0.005 0.040 445 Dihedral : 6.463 59.589 361 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 2.96 % Allowed : 14.44 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.47), residues: 305 helix: 0.69 (0.48), residues: 118 sheet: -0.18 (1.12), residues: 21 loop : -0.37 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 11 TYR 0.009 0.001 TYR J 178 PHE 0.021 0.002 PHE J 81 TRP 0.007 0.001 TRP J 132 HIS 0.004 0.001 HIS J 259 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2589) covalent geometry : angle 0.53906 ( 3509) hydrogen bonds : bond 0.03908 ( 99) hydrogen bonds : angle 5.26364 ( 279) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.114 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.4867 time to fit residues: 24.9911 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.185538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166141 restraints weight = 2670.811| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.28 r_work: 0.3968 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.146 Angle : 0.558 4.433 3509 Z= 0.287 Chirality : 0.043 0.127 387 Planarity : 0.005 0.039 445 Dihedral : 5.978 57.658 359 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.95 % Favored : 96.72 % Rotamer: Outliers : 3.33 % Allowed : 14.44 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.46), residues: 305 helix: 0.63 (0.47), residues: 118 sheet: -0.24 (1.11), residues: 21 loop : -0.42 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 11 TYR 0.013 0.002 TYR J 27 PHE 0.012 0.002 PHE J 91 TRP 0.009 0.002 TRP J 132 HIS 0.003 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2589) covalent geometry : angle 0.55776 ( 3509) hydrogen bonds : bond 0.04036 ( 99) hydrogen bonds : angle 5.16644 ( 279) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.073 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.4368 time to fit residues: 21.1193 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.184703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.165127 restraints weight = 2655.788| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.29 r_work: 0.3955 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2589 Z= 0.168 Angle : 0.581 4.213 3509 Z= 0.300 Chirality : 0.044 0.129 387 Planarity : 0.005 0.040 445 Dihedral : 5.992 57.299 359 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 4.07 % Allowed : 12.96 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.47), residues: 305 helix: 0.55 (0.47), residues: 118 sheet: -0.30 (1.12), residues: 21 loop : -0.40 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 11 TYR 0.010 0.002 TYR H 248 PHE 0.012 0.002 PHE J 91 TRP 0.010 0.002 TRP J 132 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 2589) covalent geometry : angle 0.58150 ( 3509) hydrogen bonds : bond 0.04201 ( 99) hydrogen bonds : angle 5.25311 ( 279) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: J 224 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6282 (mtt-85) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 0.5386 time to fit residues: 26.5022 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.0060 chunk 24 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 GLN ** 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 = 0.4284 r_free = 0.4284 target = 0.186345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.166646 restraints weight = 2636.176| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.31 r_work: 0.3972 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.131 Angle : 0.544 4.282 3509 Z= 0.279 Chirality : 0.043 0.128 387 Planarity : 0.005 0.040 445 Dihedral : 5.668 55.130 359 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 3.70 % Allowed : 14.44 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.47), residues: 305 helix: 0.69 (0.47), residues: 118 sheet: -0.25 (1.11), residues: 21 loop : -0.30 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 11 TYR 0.009 0.001 TYR J 178 PHE 0.025 0.002 PHE J 81 TRP 0.008 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2589) covalent geometry : angle 0.54422 ( 3509) hydrogen bonds : bond 0.03853 ( 99) hydrogen bonds : angle 5.05465 ( 279) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.082 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.5697 time to fit residues: 26.8512 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.184682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.165184 restraints weight = 2644.272| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 1.28 r_work: 0.3959 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2589 Z= 0.170 Angle : 0.585 4.259 3509 Z= 0.302 Chirality : 0.044 0.130 387 Planarity : 0.005 0.040 445 Dihedral : 5.856 56.749 359 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.93 % Favored : 95.74 % Rotamer: Outliers : 3.33 % Allowed : 15.19 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.47), residues: 305 helix: 0.60 (0.47), residues: 118 sheet: -0.34 (1.10), residues: 21 loop : -0.35 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 11 TYR 0.014 0.002 TYR J 27 PHE 0.017 0.002 PHE J 185 TRP 0.010 0.002 TRP J 132 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 2589) covalent geometry : angle 0.58453 ( 3509) hydrogen bonds : bond 0.04188 ( 99) hydrogen bonds : angle 5.19090 ( 279) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.106 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 0.5641 time to fit residues: 26.0433 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.185010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.165496 restraints weight = 2628.739| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.28 r_work: 0.3962 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2589 Z= 0.159 Angle : 0.581 4.234 3509 Z= 0.299 Chirality : 0.044 0.129 387 Planarity : 0.005 0.041 445 Dihedral : 5.772 56.128 359 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.93 % Favored : 95.74 % Rotamer: Outliers : 3.33 % Allowed : 15.19 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.47), residues: 305 helix: 0.61 (0.47), residues: 118 sheet: -0.27 (1.12), residues: 21 loop : -0.35 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 11 TYR 0.009 0.002 TYR J 190 PHE 0.014 0.002 PHE J 185 TRP 0.009 0.002 TRP J 132 HIS 0.003 0.001 HIS J 259 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 2589) covalent geometry : angle 0.58055 ( 3509) hydrogen bonds : bond 0.04108 ( 99) hydrogen bonds : angle 5.16196 ( 279) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: J 309 ARG cc_start: 0.5804 (mpt180) cc_final: 0.5393 (mpt180) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.5943 time to fit residues: 28.5511 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 11 optimal weight: 0.0060 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.187713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.168300 restraints weight = 2639.083| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.28 r_work: 0.3995 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2589 Z= 0.116 Angle : 0.540 4.085 3509 Z= 0.276 Chirality : 0.042 0.129 387 Planarity : 0.005 0.041 445 Dihedral : 5.424 53.167 359 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 3.33 % Allowed : 16.30 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.47), residues: 305 helix: 0.75 (0.47), residues: 119 sheet: -0.27 (1.12), residues: 21 loop : -0.26 (0.48), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 11 TYR 0.009 0.001 TYR J 178 PHE 0.010 0.001 PHE J 91 TRP 0.007 0.001 TRP J 132 HIS 0.003 0.001 HIS J 259 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2589) covalent geometry : angle 0.53981 ( 3509) hydrogen bonds : bond 0.03644 ( 99) hydrogen bonds : angle 4.93239 ( 279) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: J 309 ARG cc_start: 0.5802 (mpt180) cc_final: 0.5588 (mpt180) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.5994 time to fit residues: 31.9093 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 29 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.187062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167308 restraints weight = 2701.590| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.33 r_work: 0.3983 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2589 Z= 0.128 Angle : 0.555 4.131 3509 Z= 0.284 Chirality : 0.043 0.129 387 Planarity : 0.005 0.040 445 Dihedral : 5.430 54.247 359 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 2.59 % Allowed : 18.15 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.47), residues: 305 helix: 0.72 (0.47), residues: 119 sheet: -0.30 (1.11), residues: 21 loop : -0.26 (0.48), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 11 TYR 0.015 0.002 TYR J 27 PHE 0.029 0.002 PHE J 81 TRP 0.008 0.001 TRP J 132 HIS 0.003 0.001 HIS J 259 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 2589) covalent geometry : angle 0.55480 ( 3509) hydrogen bonds : bond 0.03777 ( 99) hydrogen bonds : angle 4.92687 ( 279) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.088 Fit side-chains REVERT: J 309 ARG cc_start: 0.5818 (mpt180) cc_final: 0.5604 (mpt180) outliers start: 7 outliers final: 7 residues processed: 46 average time/residue: 0.5474 time to fit residues: 25.7551 Evaluate side-chains 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.186328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166569 restraints weight = 2696.648| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.33 r_work: 0.3973 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2589 Z= 0.148 Angle : 0.590 5.744 3509 Z= 0.304 Chirality : 0.043 0.130 387 Planarity : 0.005 0.040 445 Dihedral : 5.557 55.646 359 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 2.59 % Allowed : 18.89 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.47), residues: 305 helix: 0.73 (0.47), residues: 118 sheet: -0.25 (1.12), residues: 21 loop : -0.29 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 11 TYR 0.013 0.002 TYR J 190 PHE 0.028 0.002 PHE J 81 TRP 0.008 0.002 TRP J 132 HIS 0.004 0.001 HIS J 259 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2589) covalent geometry : angle 0.59026 ( 3509) hydrogen bonds : bond 0.03966 ( 99) hydrogen bonds : angle 5.00772 ( 279) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.103 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 44 average time/residue: 0.5184 time to fit residues: 23.4031 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.186952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167191 restraints weight = 2684.473| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.33 r_work: 0.3980 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2589 Z= 0.133 Angle : 0.573 5.079 3509 Z= 0.295 Chirality : 0.043 0.130 387 Planarity : 0.005 0.041 445 Dihedral : 5.437 54.323 359 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 2.96 % Allowed : 18.52 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.47), residues: 305 helix: 0.70 (0.47), residues: 119 sheet: -0.28 (1.12), residues: 21 loop : -0.29 (0.48), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 11 TYR 0.014 0.002 TYR J 190 PHE 0.028 0.002 PHE J 81 TRP 0.007 0.001 TRP J 132 HIS 0.005 0.001 HIS J 259 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2589) covalent geometry : angle 0.57342 ( 3509) hydrogen bonds : bond 0.03818 ( 99) hydrogen bonds : angle 4.94953 ( 279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1428.54 seconds wall clock time: 25 minutes 4.82 seconds (1504.82 seconds total)