Starting phenix.real_space_refine on Tue Aug 4 12:50:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrr_18624/08_2026/8qrr_18624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrr_18624/08_2026/8qrr_18624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrr_18624/08_2026/8qrr_18624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrr_18624/08_2026/8qrr_18624.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrr_18624/08_2026/8qrr_18624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrr_18624/08_2026/8qrr_18624.cif" } resolution = 2.78 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= 1.000 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 16 5.16 5 Na 3 4.78 5 C 2052 2.51 5 N 512 2.21 5 O 546 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3129 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3116 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 16, 'TRANS': 403} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 0.91, per 1000 atoms: 0.29 Number of scatterers: 3129 At special positions: 0 Unit cell: (60.192, 70.224, 75.24, 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 16 16.00 Na 3 11.00 O 546 8.00 N 512 7.00 C 2052 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: 0.17 Conformation dependent library (CDL) restraints added in 117.1 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 85.3% 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 52 through 75 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 82 through 103 removed outlier: 3.687A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.795A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 249 through 292 removed outlier: 4.530A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.010A 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 302 Processing helix chain 'B' and resid 302 through 319 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.731A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 383 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 426 removed outlier: 4.110A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.522A pdb=" N ALA B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.640A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 210 260 hydrogen bonds defined for protein. 780 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: 0.53 Time building geometry restraints manager: 0.27 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: 988 1.34 - 1.46: 426 1.46 - 1.57: 1742 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3181 Sorted by residual: bond pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.19e-01 bond pdb=" CG LEU B 112 " pdb=" CD1 LEU B 112 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.51e-01 bond pdb=" CG LEU B 107 " pdb=" CD1 LEU B 107 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.02e-01 bond pdb=" CG1 ILE B 104 " pdb=" CD1 ILE B 104 " ideal model delta sigma weight residual 1.513 1.490 0.023 3.90e-02 6.57e+02 3.35e-01 bond pdb=" CA VAL B 472 " pdb=" C VAL B 472 " ideal model delta sigma weight residual 1.523 1.516 0.007 1.27e-02 6.20e+03 3.31e-01 ... (remaining 3176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 4214 1.12 - 2.23: 80 2.23 - 3.35: 23 3.35 - 4.47: 8 4.47 - 5.58: 7 Bond angle restraints: 4332 Sorted by residual: angle pdb=" CB ARG B 301 " pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 111.30 116.88 -5.58 2.30e+00 1.89e-01 5.89e+00 angle pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " pdb=" NE ARG B 301 " ideal model delta sigma weight residual 112.00 117.10 -5.10 2.20e+00 2.07e-01 5.37e+00 angle pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " pdb=" CG2 VAL B 459 " ideal model delta sigma weight residual 110.40 114.29 -3.89 1.70e+00 3.46e-01 5.25e+00 angle pdb=" N ILE B 103 " pdb=" CA ILE B 103 " pdb=" C ILE B 103 " ideal model delta sigma weight residual 109.34 113.04 -3.70 2.08e+00 2.31e-01 3.16e+00 angle pdb=" N VAL B 459 " pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 112.16 110.10 2.06 1.30e+00 5.92e-01 2.51e+00 ... (remaining 4327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1669 17.95 - 35.89: 166 35.89 - 53.83: 28 53.83 - 71.78: 1 71.78 - 89.72: 3 Dihedral angle restraints: 1867 sinusoidal: 681 harmonic: 1186 Sorted by residual: dihedral pdb=" CA ASP B 294 " pdb=" CB ASP B 294 " pdb=" CG ASP B 294 " pdb=" OD1 ASP B 294 " ideal model delta sinusoidal sigma weight residual -30.00 -86.47 56.47 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU B 251 " pdb=" CG GLU B 251 " pdb=" CD GLU B 251 " pdb=" OE1 GLU B 251 " ideal model delta sinusoidal sigma weight residual 0.00 85.67 -85.67 1 3.00e+01 1.11e-03 9.86e+00 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -180.00 -130.28 -49.72 3 1.50e+01 4.44e-03 8.81e+00 ... (remaining 1864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 468 0.059 - 0.118: 73 0.118 - 0.177: 1 0.177 - 0.235: 0 0.235 - 0.294: 1 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA PHE B 91 " pdb=" N PHE B 91 " pdb=" C PHE B 91 " pdb=" CB PHE B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-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 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 540 not shown) Planarity restraints: 536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 474 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C GLY B 474 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY B 474 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP B 475 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 471 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASN B 471 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN B 471 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 472 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 469 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C VAL B 469 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 469 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 470 " -0.009 2.00e-02 2.50e+03 ... (remaining 533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 617 2.77 - 3.30: 3207 3.30 - 3.83: 5511 3.83 - 4.37: 6085 4.37 - 4.90: 11075 Nonbonded interactions: 26495 Sorted by model distance: nonbonded pdb=" OD1 ASP B 388 " pdb="NA NA B 603 " model vdw 2.234 2.470 nonbonded pdb=" O PHE B 135 " pdb="NA NA B 603 " model vdw 2.255 2.470 nonbonded pdb=" OG1 THR B 139 " pdb="NA NA B 603 " model vdw 2.278 2.470 nonbonded pdb=" OD1 ASN B 386 " pdb="NA NA B 603 " model vdw 2.288 2.470 nonbonded pdb=" OG1 THR B 138 " pdb="NA NA B 603 " model vdw 2.310 2.470 ... (remaining 26490 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 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 : 0.003 0.029 3181 Z= 0.122 Angle : 0.491 5.583 4332 Z= 0.255 Chirality : 0.039 0.294 543 Planarity : 0.005 0.055 536 Dihedral : 14.324 89.721 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.21 % Allowed : 18.48 % Favored : 80.30 % 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: 2.25 (0.43), residues: 414 helix: 1.96 (0.29), residues: 340 sheet: -1.40 (1.27), residues: 20 loop : -0.25 (0.91), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 301 TYR 0.009 0.001 TYR B 334 PHE 0.008 0.001 PHE B 237 TRP 0.009 0.001 TRP B 338 HIS 0.001 0.001 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 3181) covalent geometry : angle 0.49072 / 0.26 ( 4332) hydrogen bonds : bond 0.12153 / 8.44 ( 260) hydrogen bonds : angle 5.95125 / 4.37 ( 780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.109 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.3721 time to fit residues: 17.3729 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 410 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.129395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094286 restraints weight = 3679.523| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.97 r_work: 0.2950 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.137 Angle : 0.510 6.134 4332 Z= 0.254 Chirality : 0.039 0.200 543 Planarity : 0.004 0.030 536 Dihedral : 3.798 30.958 446 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.33 % Allowed : 16.97 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.93 (0.43), residues: 414 helix: 2.43 (0.28), residues: 341 sheet: -1.37 (1.28), residues: 20 loop : 0.01 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 301 TYR 0.010 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 3181) covalent geometry : angle 0.50982 / 0.25 ( 4332) hydrogen bonds : bond 0.04370 / 2.92 ( 260) hydrogen bonds : angle 4.52619 / 3.35 ( 780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.120 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 51 average time/residue: 0.3913 time to fit residues: 20.7212 Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 4 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.2488 > 50:) chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094546 restraints weight = 3695.486| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.98 r_work: 0.2952 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3181 Z= 0.132 Angle : 0.496 5.127 4332 Z= 0.248 Chirality : 0.039 0.240 543 Planarity : 0.004 0.031 536 Dihedral : 3.233 13.286 441 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.24 % Allowed : 16.36 % Favored : 79.39 % 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: 2.95 (0.43), residues: 414 helix: 2.48 (0.28), residues: 341 sheet: -1.38 (1.30), residues: 20 loop : -0.24 (0.86), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 301 TYR 0.010 0.001 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 3181) covalent geometry : angle 0.49583 / 0.25 ( 4332) hydrogen bonds : bond 0.04085 / 2.77 ( 260) hydrogen bonds : angle 4.40890 / 3.24 ( 780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.070 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 52 average time/residue: 0.3183 time to fit residues: 17.1396 Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093772 restraints weight = 3679.027| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.97 r_work: 0.2946 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3181 Z= 0.140 Angle : 0.500 5.143 4332 Z= 0.250 Chirality : 0.040 0.253 543 Planarity : 0.004 0.031 536 Dihedral : 3.243 13.811 441 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.55 % Allowed : 15.15 % Favored : 80.30 % 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: 2.89 (0.42), residues: 414 helix: 2.48 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.95 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.002 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 3181) covalent geometry : angle 0.50032 / 0.25 ( 4332) hydrogen bonds : bond 0.04120 / 2.79 ( 260) hydrogen bonds : angle 4.40160 / 3.24 ( 780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.117 Fit side-chains REVERT: B 288 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7475 (mptp) outliers start: 15 outliers final: 4 residues processed: 48 average time/residue: 0.3635 time to fit residues: 18.2086 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095982 restraints weight = 3646.209| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.97 r_work: 0.2979 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.118 Angle : 0.486 5.313 4332 Z= 0.242 Chirality : 0.039 0.263 543 Planarity : 0.004 0.033 536 Dihedral : 3.182 11.762 441 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.64 % Allowed : 16.06 % Favored : 80.30 % 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: 3.02 (0.42), residues: 414 helix: 2.55 (0.28), residues: 341 sheet: -1.39 (1.30), residues: 20 loop : -0.42 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 301 TYR 0.008 0.001 TYR B 334 PHE 0.008 0.001 PHE B 237 TRP 0.003 0.000 TRP B 275 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 3181) covalent geometry : angle 0.48622 / 0.24 ( 4332) hydrogen bonds : bond 0.03799 / 2.58 ( 260) hydrogen bonds : angle 4.29349 / 3.15 ( 780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.066 Fit side-chains REVERT: B 253 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7929 (mt-10) outliers start: 12 outliers final: 2 residues processed: 51 average time/residue: 0.3058 time to fit residues: 16.1412 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 224 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093739 restraints weight = 3655.019| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.00 r_work: 0.2944 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3181 Z= 0.145 Angle : 0.511 5.618 4332 Z= 0.254 Chirality : 0.040 0.283 543 Planarity : 0.004 0.037 536 Dihedral : 3.234 12.811 441 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.94 % Allowed : 16.06 % Favored : 80.00 % 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: 2.90 (0.42), residues: 414 helix: 2.49 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.99 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.003 0.001 TRP B 461 HIS 0.002 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 3181) covalent geometry : angle 0.51069 / 0.25 ( 4332) hydrogen bonds : bond 0.04025 / 2.74 ( 260) hydrogen bonds : angle 4.34597 / 3.19 ( 780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.065 Fit side-chains REVERT: B 292 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6467 (mpt) outliers start: 13 outliers final: 4 residues processed: 48 average time/residue: 0.3063 time to fit residues: 15.2060 Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.0570 chunk 27 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.7526 > 50:) chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094306 restraints weight = 3690.904| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.98 r_work: 0.2953 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3181 Z= 0.137 Angle : 0.512 5.998 4332 Z= 0.254 Chirality : 0.040 0.297 543 Planarity : 0.004 0.042 536 Dihedral : 3.237 12.390 441 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.85 % Allowed : 14.85 % Favored : 80.30 % 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: 2.90 (0.42), residues: 414 helix: 2.50 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.01 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.005 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 3181) covalent geometry : angle 0.51181 / 0.25 ( 4332) hydrogen bonds : bond 0.03997 / 2.71 ( 260) hydrogen bonds : angle 4.35465 / 3.20 ( 780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.068 Fit side-chains REVERT: B 292 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6482 (mpt) outliers start: 16 outliers final: 5 residues processed: 49 average time/residue: 0.3667 time to fit residues: 18.6068 Evaluate side-chains 48 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093878 restraints weight = 3749.083| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.00 r_work: 0.2948 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3181 Z= 0.142 Angle : 0.519 6.064 4332 Z= 0.258 Chirality : 0.041 0.302 543 Planarity : 0.004 0.044 536 Dihedral : 3.244 12.631 441 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.94 % Allowed : 15.76 % Favored : 80.30 % 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: 2.81 (0.42), residues: 414 helix: 2.50 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -1.25 (0.66), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 301 TYR 0.012 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.005 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 3181) covalent geometry : angle 0.51942 / 0.26 ( 4332) hydrogen bonds : bond 0.04037 / 2.74 ( 260) hydrogen bonds : angle 4.36751 / 3.21 ( 780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.096 Fit side-chains REVERT: B 292 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6500 (mpt) outliers start: 13 outliers final: 5 residues processed: 49 average time/residue: 0.3349 time to fit residues: 17.0473 Evaluate side-chains 48 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094139 restraints weight = 3685.081| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.97 r_work: 0.2953 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3181 Z= 0.141 Angle : 0.524 6.024 4332 Z= 0.259 Chirality : 0.041 0.306 543 Planarity : 0.004 0.047 536 Dihedral : 3.257 12.555 441 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.73 % Allowed : 16.97 % Favored : 80.30 % 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: 2.89 (0.42), residues: 414 helix: 2.49 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.04 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 301 TYR 0.012 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.005 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 3181) covalent geometry : angle 0.52415 / 0.26 ( 4332) hydrogen bonds : bond 0.04031 / 2.74 ( 260) hydrogen bonds : angle 4.36733 / 3.21 ( 780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.071 Fit side-chains REVERT: B 292 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6514 (mpt) outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.3879 time to fit residues: 18.0336 Evaluate side-chains 47 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.128856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093798 restraints weight = 3654.876| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.96 r_work: 0.2945 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3181 Z= 0.143 Angle : 0.525 6.142 4332 Z= 0.260 Chirality : 0.041 0.307 543 Planarity : 0.004 0.050 536 Dihedral : 3.264 12.402 441 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.12 % Allowed : 17.58 % Favored : 80.30 % 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: 2.89 (0.42), residues: 414 helix: 2.49 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.05 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 301 TYR 0.013 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.005 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 3181) covalent geometry : angle 0.52539 / 0.26 ( 4332) hydrogen bonds : bond 0.04062 / 2.77 ( 260) hydrogen bonds : angle 4.38738 / 3.22 ( 780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.125 Fit side-chains REVERT: B 292 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6524 (mpt) outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 0.3722 time to fit residues: 17.4334 Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.7980 chunk 29 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.0332 > 50:) chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092631 restraints weight = 3715.943| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.98 r_work: 0.2925 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3181 Z= 0.154 Angle : 0.536 6.464 4332 Z= 0.266 Chirality : 0.041 0.309 543 Planarity : 0.004 0.048 536 Dihedral : 3.298 13.058 441 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.82 % Allowed : 18.18 % Favored : 80.00 % 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 (0.42), residues: 414 helix: 2.45 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.06 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 301 TYR 0.015 0.002 TYR B 334 PHE 0.012 0.001 PHE B 237 TRP 0.005 0.001 TRP B 338 HIS 0.002 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 3181) covalent geometry : angle 0.53614 / 0.27 ( 4332) hydrogen bonds : bond 0.04166 / 2.84 ( 260) hydrogen bonds : angle 4.41429 / 3.24 ( 780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1017.56 seconds wall clock time: 18 minutes 4.63 seconds (1084.63 seconds total)