Starting phenix.real_space_refine on Wed Jul 1 23:13:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rws_54346/07_2026/9rws_54346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rws_54346/07_2026/9rws_54346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rws_54346/07_2026/9rws_54346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rws_54346/07_2026/9rws_54346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rws_54346/07_2026/9rws_54346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rws_54346/07_2026/9rws_54346.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 23 5.16 5 Na 1 4.78 5 C 2607 2.51 5 N 607 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3903 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3894 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Chain breaks: 1 Time building chain proxies: 1.12, per 1000 atoms: 0.29 Number of scatterers: 3903 At special positions: 0 Unit cell: (70.4358, 62.6814, 82.7136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 Na 1 11.00 O 665 8.00 N 607 7.00 C 2607 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: 0.34 Conformation dependent library (CDL) restraints added in 146.9 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 79.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 22 through 43 removed outlier: 4.283A pdb=" N LEU A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 69 removed outlier: 3.723A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.861A pdb=" N GLY A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.863A pdb=" N LYS A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 158 through 166 removed outlier: 3.712A pdb=" N GLY A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 193 Processing helix chain 'A' and resid 195 through 213 Processing helix chain 'A' and resid 220 through 246 removed outlier: 4.068A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.828A pdb=" N ASN A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 310 through 341 removed outlier: 4.162A pdb=" N VAL A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 368 through 402 removed outlier: 3.666A pdb=" N VAL A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 438 removed outlier: 3.701A pdb=" N ILE A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 466 removed outlier: 3.648A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 449 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.727A pdb=" N GLY A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 Processing sheet with id=AA1, first strand: chain 'A' and resid 504 through 505 289 hydrogen bonds defined for protein. 858 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: 0.74 Time building geometry restraints manager: 0.44 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: 1153 1.34 - 1.46: 943 1.46 - 1.58: 1870 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 4008 Sorted by residual: bond pdb=" CG1 ILE A 227 " pdb=" CD1 ILE A 227 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.39e-01 bond pdb=" CG LEU A 190 " pdb=" CD2 LEU A 190 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.24e-01 bond pdb=" N LEU A 266 " pdb=" CA LEU A 266 " ideal model delta sigma weight residual 1.457 1.447 0.010 1.41e-02 5.03e+03 5.08e-01 bond pdb=" C ILE A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 1.334 1.350 -0.016 2.34e-02 1.83e+03 4.91e-01 bond pdb=" C SER A 115 " pdb=" N GLY A 116 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.74e-01 ... (remaining 4003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 5416 1.87 - 3.75: 47 3.75 - 5.62: 10 5.62 - 7.50: 1 7.50 - 9.37: 3 Bond angle restraints: 5477 Sorted by residual: angle pdb=" CA LEU A 531 " pdb=" CB LEU A 531 " pdb=" CG LEU A 531 " ideal model delta sigma weight residual 116.30 125.67 -9.37 3.50e+00 8.16e-02 7.17e+00 angle pdb=" CA LEU A 265 " pdb=" CB LEU A 265 " pdb=" CG LEU A 265 " ideal model delta sigma weight residual 116.30 125.46 -9.16 3.50e+00 8.16e-02 6.85e+00 angle pdb=" CA LEU A 495 " pdb=" CB LEU A 495 " pdb=" CG LEU A 495 " ideal model delta sigma weight residual 116.30 124.16 -7.86 3.50e+00 8.16e-02 5.05e+00 angle pdb=" CA TYR A 446 " pdb=" CB TYR A 446 " pdb=" CG TYR A 446 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.78e+00 angle pdb=" CA ILE A 402 " pdb=" C ILE A 402 " pdb=" N TYR A 403 " ideal model delta sigma weight residual 116.60 119.23 -2.63 1.45e+00 4.76e-01 3.28e+00 ... (remaining 5472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2006 17.67 - 35.35: 215 35.35 - 53.02: 48 53.02 - 70.70: 3 70.70 - 88.37: 2 Dihedral angle restraints: 2274 sinusoidal: 820 harmonic: 1454 Sorted by residual: dihedral pdb=" CA ASP A 343 " pdb=" CB ASP A 343 " pdb=" CG ASP A 343 " pdb=" OD1 ASP A 343 " ideal model delta sinusoidal sigma weight residual -30.00 -86.98 56.98 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " pdb=" CZ ARG A 84 " ideal model delta sinusoidal sigma weight residual -90.00 -134.41 44.41 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CA ASP A 466 " pdb=" CB ASP A 466 " pdb=" CG ASP A 466 " pdb=" OD1 ASP A 466 " ideal model delta sinusoidal sigma weight residual -30.00 -85.34 55.34 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 2271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 367 0.024 - 0.049: 143 0.049 - 0.073: 91 0.073 - 0.098: 27 0.098 - 0.122: 10 Chirality restraints: 638 Sorted by residual: chirality pdb=" CB VAL A 37 " pdb=" CA VAL A 37 " pdb=" CG1 VAL A 37 " pdb=" CG2 VAL A 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA ILE A 504 " pdb=" N ILE A 504 " pdb=" C ILE A 504 " pdb=" CB ILE A 504 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA TYR A 446 " pdb=" N TYR A 446 " pdb=" C TYR A 446 " pdb=" CB TYR A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 635 not shown) Planarity restraints: 661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 511 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 512 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.008 2.00e-02 2.50e+03 7.20e-03 1.04e+00 pdb=" CG TYR A 453 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 398 " -0.005 2.00e-02 2.50e+03 9.93e-03 9.85e-01 pdb=" C ALA A 398 " 0.017 2.00e-02 2.50e+03 pdb=" O ALA A 398 " -0.006 2.00e-02 2.50e+03 pdb=" N ALA A 399 " -0.006 2.00e-02 2.50e+03 ... (remaining 658 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 383 2.74 - 3.28: 3842 3.28 - 3.82: 7030 3.82 - 4.36: 7225 4.36 - 4.90: 13749 Nonbonded interactions: 32229 Sorted by model distance: nonbonded pdb=" OH TYR A 137 " pdb=" OG1 THR A 461 " model vdw 2.203 3.040 nonbonded pdb=" O THR A 112 " pdb=" OH TYR A 255 " model vdw 2.208 3.040 nonbonded pdb=" O VAL A 118 " pdb=" NE1 TRP A 284 " model vdw 2.275 3.120 nonbonded pdb=" OG SER A 177 " pdb=" OG SER A 390 " model vdw 2.297 3.040 nonbonded pdb=" O ILE A 525 " pdb=" OG SER A 529 " model vdw 2.310 3.040 ... (remaining 32224 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.780 Find NCS groups from input model: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.002 0.034 4008 Z= 0.106 Angle : 0.501 9.375 5477 Z= 0.235 Chirality : 0.037 0.122 638 Planarity : 0.003 0.030 661 Dihedral : 14.921 88.369 1354 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.25 % Allowed : 18.18 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.38), residues: 508 helix: 2.48 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.018 0.001 TYR A 453 PHE 0.015 0.001 PHE A 146 TRP 0.006 0.001 TRP A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 4008) covalent geometry : angle 0.50133 / 0.24 ( 5477) hydrogen bonds : bond 0.10178 / 6.23 ( 289) hydrogen bonds : angle 4.71183 / 3.42 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.141 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.0432 time to fit residues: 3.1407 Evaluate side-chains 50 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.0270 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.176824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142858 restraints weight = 4378.185| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.94 r_work: 0.3380 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4008 Z= 0.121 Angle : 0.490 7.523 5477 Z= 0.239 Chirality : 0.038 0.117 638 Planarity : 0.003 0.041 661 Dihedral : 4.147 54.884 552 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.53 % Allowed : 16.41 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.39), residues: 508 helix: 2.53 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.93 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.018 0.001 TYR A 446 PHE 0.009 0.001 PHE A 498 TRP 0.008 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4008) covalent geometry : angle 0.49027 / 0.24 ( 5477) hydrogen bonds : bond 0.03596 / 2.34 ( 289) hydrogen bonds : angle 4.03788 / 2.90 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.089 Fit side-chains REVERT: A 236 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8079 (mp) REVERT: A 259 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6272 (mtt) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.0455 time to fit residues: 3.7953 Evaluate side-chains 62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.177500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143857 restraints weight = 4317.192| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.91 r_work: 0.3407 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4008 Z= 0.103 Angle : 0.482 7.506 5477 Z= 0.229 Chirality : 0.038 0.115 638 Planarity : 0.003 0.039 661 Dihedral : 4.176 57.324 552 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.27 % Allowed : 17.68 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.39), residues: 508 helix: 2.63 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.95 (0.55), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.017 0.001 TYR A 446 PHE 0.010 0.001 PHE A 498 TRP 0.007 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 4008) covalent geometry : angle 0.48172 / 0.23 ( 5477) hydrogen bonds : bond 0.03327 / 2.15 ( 289) hydrogen bonds : angle 3.87526 / 2.81 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.130 Fit side-chains REVERT: A 236 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 259 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6252 (mtt) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 0.0436 time to fit residues: 3.9621 Evaluate side-chains 62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.177366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143602 restraints weight = 4300.979| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.91 r_work: 0.3397 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4008 Z= 0.111 Angle : 0.492 8.010 5477 Z= 0.233 Chirality : 0.038 0.117 638 Planarity : 0.003 0.040 661 Dihedral : 4.227 59.018 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.78 % Allowed : 18.69 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.39), residues: 508 helix: 2.63 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.99 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.018 0.001 TYR A 446 PHE 0.009 0.001 PHE A 498 TRP 0.007 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4008) covalent geometry : angle 0.49242 / 0.23 ( 5477) hydrogen bonds : bond 0.03298 / 2.14 ( 289) hydrogen bonds : angle 3.81968 / 2.78 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.130 Fit side-chains REVERT: A 210 TYR cc_start: 0.7064 (t80) cc_final: 0.6838 (t80) REVERT: A 259 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6272 (mtt) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.0464 time to fit residues: 4.2017 Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.170191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137425 restraints weight = 4316.399| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.87 r_work: 0.3372 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4008 Z= 0.140 Angle : 0.516 8.064 5477 Z= 0.245 Chirality : 0.039 0.124 638 Planarity : 0.003 0.040 661 Dihedral : 4.291 59.741 552 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.54 % Allowed : 18.18 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.39), residues: 508 helix: 2.52 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.01 (0.55), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 530 TYR 0.019 0.001 TYR A 446 PHE 0.013 0.001 PHE A 146 TRP 0.007 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4008) covalent geometry : angle 0.51598 / 0.24 ( 5477) hydrogen bonds : bond 0.03506 / 2.27 ( 289) hydrogen bonds : angle 3.89074 / 2.83 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.132 Fit side-chains REVERT: A 210 TYR cc_start: 0.7067 (t80) cc_final: 0.6821 (t80) REVERT: A 259 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6335 (mtt) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 0.0418 time to fit residues: 3.8598 Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.165742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132532 restraints weight = 4307.556| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.86 r_work: 0.3367 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4008 Z= 0.129 Angle : 0.515 8.384 5477 Z= 0.243 Chirality : 0.039 0.124 638 Planarity : 0.003 0.040 661 Dihedral : 4.301 59.716 552 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.28 % Allowed : 18.43 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.39), residues: 508 helix: 2.54 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.00 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 530 TYR 0.018 0.001 TYR A 446 PHE 0.011 0.001 PHE A 146 TRP 0.007 0.001 TRP A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4008) covalent geometry : angle 0.51456 / 0.24 ( 5477) hydrogen bonds : bond 0.03427 / 2.22 ( 289) hydrogen bonds : angle 3.87385 / 2.83 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.133 Fit side-chains REVERT: A 210 TYR cc_start: 0.7036 (t80) cc_final: 0.6805 (t80) REVERT: A 259 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6377 (mtt) outliers start: 13 outliers final: 10 residues processed: 64 average time/residue: 0.0464 time to fit residues: 4.1316 Evaluate side-chains 65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 29 optimal weight: 0.0670 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 47 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.175587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143161 restraints weight = 4314.912| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.86 r_work: 0.3432 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4008 Z= 0.103 Angle : 0.503 9.276 5477 Z= 0.235 Chirality : 0.038 0.124 638 Planarity : 0.003 0.040 661 Dihedral : 4.257 59.036 552 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.54 % Allowed : 17.68 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.39), residues: 508 helix: 2.60 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.94 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 530 TYR 0.016 0.001 TYR A 446 PHE 0.011 0.001 PHE A 146 TRP 0.007 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 4008) covalent geometry : angle 0.50274 / 0.24 ( 5477) hydrogen bonds : bond 0.03189 / 2.07 ( 289) hydrogen bonds : angle 3.78667 / 2.77 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.127 Fit side-chains REVERT: A 210 TYR cc_start: 0.7070 (t80) cc_final: 0.6865 (t80) REVERT: A 259 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6259 (mtt) REVERT: A 455 MET cc_start: 0.7214 (mmt) cc_final: 0.6990 (mmt) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.0416 time to fit residues: 3.9052 Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.177784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144542 restraints weight = 4294.114| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.81 r_work: 0.3416 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4008 Z= 0.125 Angle : 0.520 8.672 5477 Z= 0.243 Chirality : 0.039 0.126 638 Planarity : 0.003 0.039 661 Dihedral : 4.274 58.785 552 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.28 % Allowed : 18.43 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.39), residues: 508 helix: 2.59 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.98 (0.55), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 530 TYR 0.019 0.001 TYR A 446 PHE 0.010 0.001 PHE A 513 TRP 0.007 0.001 TRP A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4008) covalent geometry : angle 0.51993 / 0.24 ( 5477) hydrogen bonds : bond 0.03351 / 2.16 ( 289) hydrogen bonds : angle 3.82501 / 2.79 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.127 Fit side-chains REVERT: A 210 TYR cc_start: 0.7015 (t80) cc_final: 0.6811 (t80) REVERT: A 259 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6333 (mtt) outliers start: 13 outliers final: 12 residues processed: 62 average time/residue: 0.0432 time to fit residues: 3.7534 Evaluate side-chains 65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 7 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 6 optimal weight: 0.0980 chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 0.0040 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.178350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145874 restraints weight = 4315.926| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.82 r_work: 0.3426 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4008 Z= 0.092 Angle : 0.506 10.390 5477 Z= 0.233 Chirality : 0.038 0.134 638 Planarity : 0.003 0.041 661 Dihedral : 4.218 58.117 552 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.78 % Allowed : 18.43 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.39), residues: 508 helix: 2.71 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.83 (0.56), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.016 0.001 TYR A 446 PHE 0.011 0.001 PHE A 498 TRP 0.007 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 ( 4008) covalent geometry : angle 0.50577 / 0.23 ( 5477) hydrogen bonds : bond 0.03014 / 1.95 ( 289) hydrogen bonds : angle 3.70300 / 2.71 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.129 Fit side-chains REVERT: A 259 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6252 (mtt) REVERT: A 455 MET cc_start: 0.7021 (mmt) cc_final: 0.6812 (mmt) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.0485 time to fit residues: 4.0423 Evaluate side-chains 61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.175643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142949 restraints weight = 4395.619| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.84 r_work: 0.3397 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4008 Z= 0.111 Angle : 0.519 10.522 5477 Z= 0.239 Chirality : 0.038 0.131 638 Planarity : 0.003 0.041 661 Dihedral : 4.200 57.853 552 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.53 % Allowed : 18.94 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.39), residues: 508 helix: 2.67 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.85 (0.55), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.017 0.001 TYR A 446 PHE 0.010 0.001 PHE A 513 TRP 0.006 0.001 TRP A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 4008) covalent geometry : angle 0.51879 / 0.24 ( 5477) hydrogen bonds : bond 0.03184 / 2.06 ( 289) hydrogen bonds : angle 3.73720 / 2.73 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.128 Fit side-chains REVERT: A 259 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6270 (mtt) REVERT: A 455 MET cc_start: 0.7107 (mmt) cc_final: 0.6887 (mmt) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.0393 time to fit residues: 3.4033 Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.173593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140766 restraints weight = 4380.383| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.84 r_work: 0.3369 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4008 Z= 0.131 Angle : 0.534 10.614 5477 Z= 0.247 Chirality : 0.039 0.131 638 Planarity : 0.003 0.040 661 Dihedral : 4.241 57.855 552 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.03 % Allowed : 18.43 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.39), residues: 508 helix: 2.59 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.94 (0.56), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.019 0.001 TYR A 446 PHE 0.011 0.001 PHE A 513 TRP 0.008 0.001 TRP A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 4008) covalent geometry : angle 0.53409 / 0.25 ( 5477) hydrogen bonds : bond 0.03383 / 2.20 ( 289) hydrogen bonds : angle 3.81483 / 2.79 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 977.31 seconds wall clock time: 17 minutes 26.51 seconds (1046.51 seconds total)