Starting phenix.real_space_refine on Fri Aug 22 13:15:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrw_18628/08_2025/8qrw_18628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrw_18628/08_2025/8qrw_18628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrw_18628/08_2025/8qrw_18628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrw_18628/08_2025/8qrw_18628.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrw_18628/08_2025/8qrw_18628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrw_18628/08_2025/8qrw_18628.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.594 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 15 5.16 5 Na 1 4.78 5 C 2044 2.51 5 N 509 2.21 5 O 542 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3111 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3110 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 16, 'TRANS': 402} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.05, per 1000 atoms: 0.34 Number of scatterers: 3111 At special positions: 0 Unit cell: (68.474, 61.32, 74.606, 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 15 16.00 Na 1 11.00 O 542 8.00 N 509 7.00 C 2044 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: 0.27 Conformation dependent library (CDL) restraints added in 123.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 86.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 49 through 75 removed outlier: 4.002A pdb=" N VAL B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 118 removed outlier: 3.526A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) Proline residue: B 83 - end of helix Proline residue: B 92 - end of helix removed outlier: 3.639A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix Processing helix chain 'B' and resid 120 through 152 Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.506A pdb=" N PHE B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.654A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 291 removed outlier: 3.814A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 294 through 319 removed outlier: 5.611A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.596A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 3.680A pdb=" N THR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 removed outlier: 3.908A pdb=" N PHE B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) Proline residue: B 380 - end of helix removed outlier: 3.737A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 426 removed outlier: 4.029A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.925A pdb=" N VAL B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 458 removed outlier: 3.747A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 487 removed outlier: 4.446A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 210 252 hydrogen bonds defined for protein. 756 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: 0.51 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 984 1.34 - 1.46: 413 1.46 - 1.57: 1745 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3166 Sorted by residual: bond pdb=" C ASN B 447 " pdb=" N LEU B 448 " ideal model delta sigma weight residual 1.333 1.370 -0.037 2.74e-02 1.33e+03 1.84e+00 bond pdb=" CA VAL B 220 " pdb=" CB VAL B 220 " ideal model delta sigma weight residual 1.537 1.527 0.010 1.29e-02 6.01e+03 6.47e-01 bond pdb=" CB ASN B 332 " pdb=" CG ASN B 332 " ideal model delta sigma weight residual 1.516 1.533 -0.017 2.50e-02 1.60e+03 4.66e-01 bond pdb=" CG LEU B 112 " pdb=" CD1 LEU B 112 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.44e-01 bond pdb=" CA MET B 387 " pdb=" C MET B 387 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.61e-02 3.86e+03 3.20e-01 ... (remaining 3161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 4039 0.86 - 1.71: 221 1.71 - 2.57: 32 2.57 - 3.42: 12 3.42 - 4.28: 9 Bond angle restraints: 4313 Sorted by residual: angle pdb=" N THR B 207 " pdb=" CA THR B 207 " pdb=" C THR B 207 " ideal model delta sigma weight residual 109.95 107.48 2.47 1.44e+00 4.82e-01 2.95e+00 angle pdb=" N VAL B 385 " pdb=" CA VAL B 385 " pdb=" C VAL B 385 " ideal model delta sigma weight residual 109.34 112.66 -3.32 2.08e+00 2.31e-01 2.55e+00 angle pdb=" N ALA B 157 " pdb=" CA ALA B 157 " pdb=" C ALA B 157 " ideal model delta sigma weight residual 112.57 110.96 1.61 1.13e+00 7.83e-01 2.03e+00 angle pdb=" CA LEU B 105 " pdb=" C LEU B 105 " pdb=" N PRO B 106 " ideal model delta sigma weight residual 118.44 120.52 -2.08 1.59e+00 3.96e-01 1.71e+00 angle pdb=" CB LYS B 247 " pdb=" CG LYS B 247 " pdb=" CD LYS B 247 " ideal model delta sigma weight residual 111.30 114.28 -2.98 2.30e+00 1.89e-01 1.68e+00 ... (remaining 4308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 1658 15.24 - 30.48: 139 30.48 - 45.72: 47 45.72 - 60.96: 10 60.96 - 76.20: 3 Dihedral angle restraints: 1857 sinusoidal: 676 harmonic: 1181 Sorted by residual: dihedral pdb=" CA LEU B 151 " pdb=" C LEU B 151 " pdb=" N ALA B 152 " pdb=" CA ALA B 152 " ideal model delta harmonic sigma weight residual 180.00 163.79 16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ARG B 330 " pdb=" CB ARG B 330 " pdb=" CG ARG B 330 " pdb=" CD ARG B 330 " ideal model delta sinusoidal sigma weight residual -60.00 -116.24 56.24 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CG ARG B 330 " pdb=" CD ARG B 330 " pdb=" NE ARG B 330 " pdb=" CZ ARG B 330 " ideal model delta sinusoidal sigma weight residual -180.00 -138.62 -41.38 2 1.50e+01 4.44e-03 9.32e+00 ... (remaining 1854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 357 0.025 - 0.049: 93 0.049 - 0.073: 56 0.073 - 0.098: 30 0.098 - 0.122: 5 Chirality restraints: 541 Sorted by residual: chirality pdb=" CA PRO B 121 " pdb=" N PRO B 121 " pdb=" C PRO B 121 " pdb=" CB PRO B 121 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA VAL B 222 " pdb=" N VAL B 222 " pdb=" C VAL B 222 " pdb=" CB VAL B 222 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.06e-01 ... (remaining 538 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 120 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO B 121 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 342 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO B 343 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 343 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 343 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 211 " -0.127 9.50e-02 1.11e+02 5.72e-02 2.31e+00 pdb=" NE ARG B 211 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 211 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 211 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 211 " -0.001 2.00e-02 2.50e+03 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 169 2.73 - 3.27: 3313 3.27 - 3.82: 5360 3.82 - 4.36: 5904 4.36 - 4.90: 10773 Nonbonded interactions: 25519 Sorted by model distance: nonbonded pdb=" O ASN B 471 " pdb="NA NA B 601 " model vdw 2.188 2.470 nonbonded pdb=" O ASN B 386 " pdb="NA NA B 601 " model vdw 2.241 2.470 nonbonded pdb=" OD2 ASP B 182 " pdb=" OH TYR B 208 " model vdw 2.377 3.040 nonbonded pdb=" O VAL B 463 " pdb=" OG SER B 466 " model vdw 2.405 3.040 nonbonded pdb=" N ASP B 410 " pdb=" OD1 ASP B 410 " model vdw 2.428 3.120 ... (remaining 25514 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: 1.560 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.360 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:9.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 0.037 3166 Z= 0.120 Angle : 0.497 4.281 4313 Z= 0.285 Chirality : 0.035 0.122 541 Planarity : 0.005 0.057 533 Dihedral : 13.750 76.201 1099 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % 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 aren not related in a simple way. whole: 2.07 (0.44), residues: 413 helix: 1.85 (0.31), residues: 330 sheet: -1.03 (1.22), residues: 20 loop : -0.21 (0.82), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 211 TYR 0.007 0.001 TYR B 334 PHE 0.006 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3166) covalent geometry : angle 0.49661 ( 4313) hydrogen bonds : bond 0.11920 ( 252) hydrogen bonds : angle 5.99954 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.130 Fit side-chains REVERT: B 362 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8156 (ttpp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.4905 time to fit residues: 21.2159 Evaluate side-chains 33 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0030 chunk 37 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.138662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105370 restraints weight = 3639.105| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.79 r_work: 0.2914 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3166 Z= 0.128 Angle : 0.525 6.952 4313 Z= 0.263 Chirality : 0.037 0.129 541 Planarity : 0.005 0.054 533 Dihedral : 3.637 13.972 439 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.66 % Allowed : 9.45 % Favored : 86.89 % 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 aren not related in a simple way. whole: 2.57 (0.42), residues: 413 helix: 2.12 (0.29), residues: 341 sheet: -0.93 (1.25), residues: 20 loop : 0.15 (0.82), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.008 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.007 0.001 TRP B 461 HIS 0.001 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3166) covalent geometry : angle 0.52537 ( 4313) hydrogen bonds : bond 0.04371 ( 252) hydrogen bonds : angle 4.45253 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.067 Fit side-chains REVERT: B 132 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7549 (mm) REVERT: B 209 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7072 (mt-10) outliers start: 12 outliers final: 3 residues processed: 45 average time/residue: 0.3818 time to fit residues: 17.7323 Evaluate side-chains 37 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.0170 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.137899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105418 restraints weight = 3616.073| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.69 r_work: 0.2992 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3166 Z= 0.131 Angle : 0.541 13.287 4313 Z= 0.260 Chirality : 0.038 0.135 541 Planarity : 0.005 0.052 533 Dihedral : 3.567 13.356 439 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.35 % Allowed : 10.67 % Favored : 85.98 % 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 aren not related in a simple way. whole: 2.64 (0.42), residues: 413 helix: 2.16 (0.28), residues: 340 sheet: -0.94 (1.26), residues: 20 loop : 0.28 (0.80), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 211 TYR 0.011 0.001 TYR B 334 PHE 0.008 0.001 PHE B 89 TRP 0.006 0.001 TRP B 461 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3166) covalent geometry : angle 0.54071 ( 4313) hydrogen bonds : bond 0.04190 ( 252) hydrogen bonds : angle 4.29114 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.078 Fit side-chains REVERT: B 132 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7515 (mm) REVERT: B 209 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7015 (mt-10) REVERT: B 356 THR cc_start: 0.8469 (p) cc_final: 0.8097 (t) REVERT: B 441 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.7023 (mt) outliers start: 11 outliers final: 3 residues processed: 41 average time/residue: 0.4355 time to fit residues: 18.3389 Evaluate side-chains 39 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 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 = 0.3527 r_free = 0.3527 target = 0.136720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104664 restraints weight = 3599.646| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.66 r_work: 0.2983 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3166 Z= 0.142 Angle : 0.563 16.116 4313 Z= 0.263 Chirality : 0.038 0.125 541 Planarity : 0.004 0.049 533 Dihedral : 3.561 13.358 439 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.66 % Allowed : 11.28 % Favored : 85.06 % 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 aren not related in a simple way. whole: 2.54 (0.41), residues: 413 helix: 2.13 (0.28), residues: 339 sheet: -0.93 (1.26), residues: 20 loop : -0.06 (0.76), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.012 0.001 TYR B 334 PHE 0.009 0.001 PHE B 237 TRP 0.005 0.001 TRP B 461 HIS 0.001 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3166) covalent geometry : angle 0.56295 ( 4313) hydrogen bonds : bond 0.04282 ( 252) hydrogen bonds : angle 4.26926 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.080 Fit side-chains REVERT: B 132 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7506 (mm) REVERT: B 209 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: B 356 THR cc_start: 0.8468 (p) cc_final: 0.8104 (t) REVERT: B 441 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7033 (mt) outliers start: 12 outliers final: 2 residues processed: 41 average time/residue: 0.4643 time to fit residues: 19.5841 Evaluate side-chains 37 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.138199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105798 restraints weight = 3583.638| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.67 r_work: 0.3017 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3166 Z= 0.123 Angle : 0.536 15.837 4313 Z= 0.250 Chirality : 0.037 0.123 541 Planarity : 0.004 0.047 533 Dihedral : 3.471 13.173 439 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.74 % Allowed : 12.80 % Favored : 84.45 % 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 aren not related in a simple way. whole: 2.66 (0.42), residues: 413 helix: 2.19 (0.28), residues: 340 sheet: -0.82 (1.29), residues: 20 loop : 0.10 (0.79), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.009 0.001 TYR B 334 PHE 0.007 0.001 PHE B 89 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3166) covalent geometry : angle 0.53553 ( 4313) hydrogen bonds : bond 0.03920 ( 252) hydrogen bonds : angle 4.15381 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.070 Fit side-chains REVERT: B 132 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7412 (mm) REVERT: B 209 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: B 356 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8065 (t) outliers start: 9 outliers final: 2 residues processed: 40 average time/residue: 0.3566 time to fit residues: 14.7546 Evaluate side-chains 36 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.138812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105856 restraints weight = 3579.321| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.72 r_work: 0.3002 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3166 Z= 0.118 Angle : 0.548 17.304 4313 Z= 0.252 Chirality : 0.037 0.120 541 Planarity : 0.004 0.046 533 Dihedral : 3.412 13.044 439 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.05 % Allowed : 13.72 % Favored : 83.23 % 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 aren not related in a simple way. whole: 2.79 (0.42), residues: 413 helix: 2.29 (0.28), residues: 340 sheet: -0.83 (1.30), residues: 20 loop : 0.09 (0.80), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.009 0.001 TYR B 334 PHE 0.008 0.001 PHE B 89 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3166) covalent geometry : angle 0.54803 ( 4313) hydrogen bonds : bond 0.03827 ( 252) hydrogen bonds : angle 4.12336 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.080 Fit side-chains REVERT: B 132 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7509 (mm) REVERT: B 209 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: B 356 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8175 (t) outliers start: 10 outliers final: 2 residues processed: 42 average time/residue: 0.3223 time to fit residues: 14.0635 Evaluate side-chains 37 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.137672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104030 restraints weight = 3652.491| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.80 r_work: 0.2941 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3166 Z= 0.136 Angle : 0.573 18.338 4313 Z= 0.263 Chirality : 0.038 0.141 541 Planarity : 0.004 0.045 533 Dihedral : 3.458 13.025 439 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.13 % Allowed : 14.94 % Favored : 82.93 % 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 aren not related in a simple way. whole: 2.66 (0.42), residues: 413 helix: 2.22 (0.28), residues: 340 sheet: -0.85 (1.30), residues: 20 loop : -0.09 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.008 0.001 PHE B 237 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3166) covalent geometry : angle 0.57271 ( 4313) hydrogen bonds : bond 0.04089 ( 252) hydrogen bonds : angle 4.20704 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.081 Fit side-chains REVERT: B 132 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7664 (mm) REVERT: B 209 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: B 356 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8282 (t) outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 0.4008 time to fit residues: 15.3055 Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.139379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106683 restraints weight = 3648.953| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.69 r_work: 0.2998 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3166 Z= 0.115 Angle : 0.552 17.567 4313 Z= 0.254 Chirality : 0.037 0.139 541 Planarity : 0.004 0.044 533 Dihedral : 3.384 12.817 439 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.74 % Allowed : 14.33 % Favored : 82.93 % 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 aren not related in a simple way. whole: 2.77 (0.42), residues: 413 helix: 2.29 (0.28), residues: 341 sheet: -0.83 (1.32), residues: 20 loop : -0.06 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.008 0.001 TYR B 334 PHE 0.007 0.001 PHE B 89 TRP 0.006 0.001 TRP B 338 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3166) covalent geometry : angle 0.55191 ( 4313) hydrogen bonds : bond 0.03733 ( 252) hydrogen bonds : angle 4.14287 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.088 Fit side-chains REVERT: B 132 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7345 (mm) REVERT: B 209 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: B 356 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8091 (t) outliers start: 9 outliers final: 2 residues processed: 39 average time/residue: 0.3825 time to fit residues: 15.4710 Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.138584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.105786 restraints weight = 3645.221| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.68 r_work: 0.3001 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3166 Z= 0.130 Angle : 0.564 17.233 4313 Z= 0.262 Chirality : 0.038 0.131 541 Planarity : 0.004 0.043 533 Dihedral : 3.418 12.865 439 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.13 % Allowed : 15.24 % Favored : 82.62 % 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 aren not related in a simple way. whole: 2.75 (0.42), residues: 413 helix: 2.28 (0.28), residues: 341 sheet: -0.85 (1.32), residues: 20 loop : -0.11 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.008 0.001 PHE B 237 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3166) covalent geometry : angle 0.56410 ( 4313) hydrogen bonds : bond 0.03975 ( 252) hydrogen bonds : angle 4.21441 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.068 Fit side-chains REVERT: B 132 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7377 (mm) REVERT: B 209 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: B 356 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8157 (t) outliers start: 7 outliers final: 3 residues processed: 39 average time/residue: 0.4160 time to fit residues: 16.7354 Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.139318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106400 restraints weight = 3595.255| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.69 r_work: 0.3009 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3166 Z= 0.122 Angle : 0.555 17.032 4313 Z= 0.259 Chirality : 0.037 0.128 541 Planarity : 0.004 0.043 533 Dihedral : 3.399 12.826 439 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.83 % Allowed : 15.85 % Favored : 82.32 % 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 aren not related in a simple way. whole: 2.79 (0.42), residues: 413 helix: 2.29 (0.28), residues: 342 sheet: -0.84 (1.32), residues: 20 loop : -0.05 (0.84), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 211 TYR 0.009 0.001 TYR B 334 PHE 0.007 0.001 PHE B 237 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3166) covalent geometry : angle 0.55546 ( 4313) hydrogen bonds : bond 0.03834 ( 252) hydrogen bonds : angle 4.18897 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.067 Fit side-chains REVERT: B 132 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7453 (mm) REVERT: B 209 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: B 356 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8142 (t) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.3836 time to fit residues: 15.4754 Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.0040 chunk 19 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.138944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105690 restraints weight = 3661.853| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.71 r_work: 0.2984 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3166 Z= 0.129 Angle : 0.569 16.922 4313 Z= 0.266 Chirality : 0.038 0.125 541 Planarity : 0.004 0.042 533 Dihedral : 3.413 12.759 439 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.13 % Allowed : 15.24 % Favored : 82.62 % 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 aren not related in a simple way. whole: 2.74 (0.42), residues: 413 helix: 2.28 (0.28), residues: 341 sheet: -0.91 (1.32), residues: 20 loop : -0.16 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 211 TYR 0.010 0.001 TYR B 334 PHE 0.008 0.001 PHE B 237 TRP 0.007 0.001 TRP B 275 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3166) covalent geometry : angle 0.56915 ( 4313) hydrogen bonds : bond 0.03965 ( 252) hydrogen bonds : angle 4.19003 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 974.51 seconds wall clock time: 17 minutes 20.79 seconds (1040.79 seconds total)