Starting phenix.real_space_refine on Fri May 9 18:36:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3f_41860/05_2025/8u3f_41860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3f_41860/05_2025/8u3f_41860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3f_41860/05_2025/8u3f_41860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3f_41860/05_2025/8u3f_41860.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3f_41860/05_2025/8u3f_41860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3f_41860/05_2025/8u3f_41860.cif" } resolution = 3.31 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= 0.002 sd= 0.073 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 17 5.16 5 C 2274 2.51 5 N 534 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3410 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3410 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 19, 'TRANS': 417} Chain breaks: 2 Time building chain proxies: 2.83, per 1000 atoms: 0.83 Number of scatterers: 3410 At special positions: 0 Unit cell: (58.1, 64.74, 86.32, 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 17 16.00 O 585 8.00 N 534 7.00 C 2274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 387 " distance=2.03 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: 0.86 Conformation dependent library (CDL) restraints added in 423.5 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 37 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 134 through 151 removed outlier: 4.555A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.635A pdb=" N ASP A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.506A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Proline residue: A 215 - end of helix removed outlier: 3.712A pdb=" N GLY A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 248 removed outlier: 3.648A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 288 through 311 removed outlier: 3.743A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 332 through 356 Processing helix chain 'A' and resid 359 through 384 Proline residue: A 375 - end of helix removed outlier: 3.614A pdb=" N GLY A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 403 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.636A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.712A pdb=" N PHE A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 483 through 487 239 hydrogen bonds defined for protein. 702 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: 0.97 Time building geometry restraints manager: 1.03 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: 1002 1.34 - 1.46: 920 1.46 - 1.58: 1565 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3513 Sorted by residual: bond pdb=" CA VAL A 280 " pdb=" CB VAL A 280 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.50e-01 bond pdb=" N PRO A 84 " pdb=" CA PRO A 84 " ideal model delta sigma weight residual 1.469 1.476 -0.007 7.40e-03 1.83e+04 9.44e-01 bond pdb=" CA ASN A 323 " pdb=" C ASN A 323 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.66e-01 bond pdb=" N GLY A 134 " pdb=" CA GLY A 134 " ideal model delta sigma weight residual 1.447 1.457 -0.011 1.18e-02 7.18e+03 8.22e-01 bond pdb=" CB VAL A 211 " pdb=" CG2 VAL A 211 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.47e-01 ... (remaining 3508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 4434 1.05 - 2.10: 286 2.10 - 3.15: 44 3.15 - 4.20: 21 4.20 - 5.25: 6 Bond angle restraints: 4791 Sorted by residual: angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 109.34 113.83 -4.49 2.08e+00 2.31e-01 4.66e+00 angle pdb=" C LEU A 447 " pdb=" N THR A 448 " pdb=" CA THR A 448 " ideal model delta sigma weight residual 122.89 120.51 2.38 1.12e+00 7.97e-01 4.51e+00 angle pdb=" CA THR A 153 " pdb=" C THR A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 118.44 121.64 -3.20 1.59e+00 3.96e-01 4.05e+00 angle pdb=" N VAL A 58 " pdb=" CA VAL A 58 " pdb=" C VAL A 58 " ideal model delta sigma weight residual 109.34 113.48 -4.14 2.08e+00 2.31e-01 3.97e+00 angle pdb=" CA LEU A 289 " pdb=" C LEU A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 118.44 121.58 -3.14 1.59e+00 3.96e-01 3.91e+00 ... (remaining 4786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 1771 16.48 - 32.95: 182 32.95 - 49.43: 30 49.43 - 65.90: 3 65.90 - 82.38: 1 Dihedral angle restraints: 1987 sinusoidal: 737 harmonic: 1250 Sorted by residual: dihedral pdb=" CA ASN A 323 " pdb=" C ASN A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual 180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASN A 323 " pdb=" CB ASN A 323 " pdb=" CG ASN A 323 " pdb=" OD1 ASN A 323 " ideal model delta sinusoidal sigma weight residual -90.00 -152.99 62.99 2 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CG LYS A 278 " pdb=" CD LYS A 278 " pdb=" CE LYS A 278 " pdb=" NZ LYS A 278 " ideal model delta sinusoidal sigma weight residual -180.00 -136.68 -43.32 3 1.50e+01 4.44e-03 7.79e+00 ... (remaining 1984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 356 0.037 - 0.073: 148 0.073 - 0.110: 33 0.110 - 0.146: 6 0.146 - 0.183: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA PHE A 305 " pdb=" N PHE A 305 " pdb=" C PHE A 305 " pdb=" CB PHE A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA PRO A 192 " pdb=" N PRO A 192 " pdb=" C PRO A 192 " pdb=" CB PRO A 192 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA PRO A 375 " pdb=" N PRO A 375 " pdb=" C PRO A 375 " pdb=" CB PRO A 375 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 541 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 305 " 0.014 2.00e-02 2.50e+03 1.40e-02 3.45e+00 pdb=" CG PHE A 305 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 305 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 305 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 305 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 305 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 305 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 290 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 163 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.022 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 911 2.79 - 3.32: 3343 3.32 - 3.85: 5797 3.85 - 4.37: 6821 4.37 - 4.90: 11982 Nonbonded interactions: 28854 Sorted by model distance: nonbonded pdb=" NH2 ARG A 57 " pdb=" OE2 GLU A 175 " model vdw 2.265 3.120 nonbonded pdb=" OH TYR A 101 " pdb=" OD1 ASP A 158 " model vdw 2.286 3.040 nonbonded pdb=" O PRO A 192 " pdb=" NH2 ARG A 353 " model vdw 2.314 3.120 nonbonded pdb=" OG SER A 37 " pdb=" OE2 GLU A 262 " model vdw 2.352 3.040 nonbonded pdb=" O ALA A 444 " pdb=" OG1 THR A 448 " model vdw 2.358 3.040 ... (remaining 28849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.360 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 0.038 3514 Z= 0.197 Angle : 0.625 5.254 4793 Z= 0.369 Chirality : 0.041 0.183 544 Planarity : 0.005 0.046 581 Dihedral : 12.988 82.377 1188 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.37), residues: 431 helix: -0.90 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -0.82 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.006 0.001 HIS A 298 PHE 0.032 0.002 PHE A 305 TYR 0.011 0.001 TYR A 306 ARG 0.003 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.16164 ( 239) hydrogen bonds : angle 6.20821 ( 702) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.40530 ( 2) covalent geometry : bond 0.00462 ( 3513) covalent geometry : angle 0.62481 ( 4791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.383 Fit side-chains REVERT: A 256 LYS cc_start: 0.5750 (mmtt) cc_final: 0.4278 (tttp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1885 time to fit residues: 9.8670 Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.0010 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103343 restraints weight = 3863.049| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.76 r_work: 0.3011 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3514 Z= 0.131 Angle : 0.544 5.323 4793 Z= 0.289 Chirality : 0.040 0.114 544 Planarity : 0.005 0.044 581 Dihedral : 4.248 20.132 463 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.55 % Allowed : 9.70 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.40), residues: 431 helix: 0.61 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.12 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.011 0.001 PHE A 305 TYR 0.012 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 239) hydrogen bonds : angle 4.52626 ( 702) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.75644 ( 2) covalent geometry : bond 0.00282 ( 3513) covalent geometry : angle 0.54435 ( 4791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.357 Fit side-chains REVERT: A 256 LYS cc_start: 0.6167 (mmtt) cc_final: 0.3978 (tttp) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.1881 time to fit residues: 8.1634 Evaluate side-chains 32 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.138260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.103233 restraints weight = 3867.518| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.77 r_work: 0.3004 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3514 Z= 0.149 Angle : 0.547 5.223 4793 Z= 0.286 Chirality : 0.041 0.115 544 Planarity : 0.005 0.042 581 Dihedral : 4.246 21.987 463 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.11 % Allowed : 12.19 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.40), residues: 431 helix: 1.12 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.08 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.015 0.001 PHE A 322 TYR 0.011 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 239) hydrogen bonds : angle 4.37924 ( 702) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.78096 ( 2) covalent geometry : bond 0.00353 ( 3513) covalent geometry : angle 0.54735 ( 4791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.379 Fit side-chains REVERT: A 256 LYS cc_start: 0.6170 (mmtt) cc_final: 0.4012 (tttp) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.2003 time to fit residues: 9.0534 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.140418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104551 restraints weight = 3903.312| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.83 r_work: 0.3011 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3514 Z= 0.125 Angle : 0.530 5.212 4793 Z= 0.275 Chirality : 0.040 0.113 544 Planarity : 0.005 0.042 581 Dihedral : 4.193 21.286 463 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.66 % Allowed : 12.74 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.41), residues: 431 helix: 1.46 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -0.92 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.026 0.001 PHE A 322 TYR 0.011 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 239) hydrogen bonds : angle 4.29018 ( 702) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.79554 ( 2) covalent geometry : bond 0.00283 ( 3513) covalent geometry : angle 0.53014 ( 4791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.338 Fit side-chains REVERT: A 256 LYS cc_start: 0.6160 (mmtt) cc_final: 0.3985 (tttp) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.1682 time to fit residues: 7.8221 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.138937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.103248 restraints weight = 3956.806| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.80 r_work: 0.2991 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3514 Z= 0.143 Angle : 0.536 5.229 4793 Z= 0.278 Chirality : 0.041 0.115 544 Planarity : 0.005 0.043 581 Dihedral : 4.188 21.787 463 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.66 % Allowed : 13.57 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.41), residues: 431 helix: 1.55 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.76 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.028 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 239) hydrogen bonds : angle 4.25423 ( 702) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.78101 ( 2) covalent geometry : bond 0.00339 ( 3513) covalent geometry : angle 0.53591 ( 4791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.328 Fit side-chains REVERT: A 256 LYS cc_start: 0.6261 (mmtt) cc_final: 0.4011 (tttp) REVERT: A 257 ARG cc_start: 0.8327 (mtm110) cc_final: 0.7733 (ttm110) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.1695 time to fit residues: 7.4615 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 0.0030 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.104132 restraints weight = 3935.938| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.80 r_work: 0.3016 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3514 Z= 0.120 Angle : 0.516 5.204 4793 Z= 0.267 Chirality : 0.039 0.117 544 Planarity : 0.005 0.043 581 Dihedral : 4.115 22.334 463 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.77 % Allowed : 13.85 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.41), residues: 431 helix: 1.76 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.64 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.022 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 239) hydrogen bonds : angle 4.18716 ( 702) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.65194 ( 2) covalent geometry : bond 0.00270 ( 3513) covalent geometry : angle 0.51628 ( 4791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.352 Fit side-chains REVERT: A 256 LYS cc_start: 0.6183 (mmtt) cc_final: 0.3944 (tttp) REVERT: A 257 ARG cc_start: 0.8272 (mtm110) cc_final: 0.7852 (ttm110) outliers start: 10 outliers final: 7 residues processed: 37 average time/residue: 0.1448 time to fit residues: 6.9743 Evaluate side-chains 34 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104133 restraints weight = 3877.938| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.81 r_work: 0.3017 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3514 Z= 0.130 Angle : 0.532 6.671 4793 Z= 0.273 Chirality : 0.040 0.116 544 Planarity : 0.005 0.043 581 Dihedral : 4.117 22.516 463 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 14.68 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.41), residues: 431 helix: 1.78 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.56 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.003 0.001 HIS A 298 PHE 0.019 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 239) hydrogen bonds : angle 4.17560 ( 702) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.66096 ( 2) covalent geometry : bond 0.00304 ( 3513) covalent geometry : angle 0.53161 ( 4791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.342 Fit side-chains REVERT: A 256 LYS cc_start: 0.6243 (mmtt) cc_final: 0.4003 (tttp) REVERT: A 257 ARG cc_start: 0.8285 (mtm110) cc_final: 0.7904 (ttm110) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.1508 time to fit residues: 6.8284 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.139113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103512 restraints weight = 3923.532| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.78 r_work: 0.3008 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3514 Z= 0.141 Angle : 0.537 6.148 4793 Z= 0.276 Chirality : 0.040 0.123 544 Planarity : 0.005 0.044 581 Dihedral : 4.153 22.127 463 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 14.68 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.41), residues: 431 helix: 1.79 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.55 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.003 0.001 HIS A 298 PHE 0.032 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 239) hydrogen bonds : angle 4.19461 ( 702) SS BOND : bond 0.00118 ( 1) SS BOND : angle 0.72746 ( 2) covalent geometry : bond 0.00334 ( 3513) covalent geometry : angle 0.53647 ( 4791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.329 Fit side-chains REVERT: A 256 LYS cc_start: 0.6316 (mmtt) cc_final: 0.4082 (tttp) REVERT: A 257 ARG cc_start: 0.8293 (mtm110) cc_final: 0.7936 (ttm110) REVERT: A 305 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7019 (t80) outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.1474 time to fit residues: 6.3048 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.138779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103373 restraints weight = 3835.982| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.76 r_work: 0.3008 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3514 Z= 0.143 Angle : 0.537 6.162 4793 Z= 0.277 Chirality : 0.040 0.126 544 Planarity : 0.005 0.044 581 Dihedral : 4.166 22.201 463 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.77 % Allowed : 14.40 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.41), residues: 431 helix: 1.81 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.48 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.003 0.001 HIS A 298 PHE 0.030 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 239) hydrogen bonds : angle 4.19409 ( 702) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.62769 ( 2) covalent geometry : bond 0.00339 ( 3513) covalent geometry : angle 0.53734 ( 4791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.334 Fit side-chains REVERT: A 256 LYS cc_start: 0.6347 (mmtt) cc_final: 0.4176 (tttp) REVERT: A 257 ARG cc_start: 0.8289 (mtm110) cc_final: 0.7948 (ttm110) REVERT: A 305 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6972 (t80) REVERT: A 329 PHE cc_start: 0.5666 (m-80) cc_final: 0.5418 (m-80) outliers start: 10 outliers final: 8 residues processed: 35 average time/residue: 0.1438 time to fit residues: 6.5369 Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 14 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105280 restraints weight = 3895.468| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.00 r_work: 0.3007 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3514 Z= 0.119 Angle : 0.521 6.217 4793 Z= 0.268 Chirality : 0.039 0.112 544 Planarity : 0.005 0.044 581 Dihedral : 4.112 22.160 463 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 14.40 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.41), residues: 431 helix: 1.90 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.41 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.029 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 239) hydrogen bonds : angle 4.16354 ( 702) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.56619 ( 2) covalent geometry : bond 0.00271 ( 3513) covalent geometry : angle 0.52139 ( 4791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.340 Fit side-chains REVERT: A 256 LYS cc_start: 0.6280 (mmtt) cc_final: 0.4000 (tttp) REVERT: A 257 ARG cc_start: 0.8275 (mtm110) cc_final: 0.7899 (ttm110) REVERT: A 305 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7091 (t80) REVERT: A 329 PHE cc_start: 0.5540 (m-80) cc_final: 0.5298 (m-80) outliers start: 9 outliers final: 7 residues processed: 36 average time/residue: 0.1526 time to fit residues: 7.1434 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.139841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104067 restraints weight = 3900.229| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.01 r_work: 0.2992 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3514 Z= 0.145 Angle : 0.543 5.988 4793 Z= 0.280 Chirality : 0.040 0.115 544 Planarity : 0.005 0.044 581 Dihedral : 4.142 22.198 463 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 14.96 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.41), residues: 431 helix: 1.84 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.38 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.029 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 239) hydrogen bonds : angle 4.19469 ( 702) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.58944 ( 2) covalent geometry : bond 0.00348 ( 3513) covalent geometry : angle 0.54311 ( 4791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.41 seconds wall clock time: 34 minutes 58.32 seconds (2098.32 seconds total)