Starting phenix.real_space_refine on Wed Jul 1 23:55:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kts_62564/07_2026/9kts_62564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kts_62564/07_2026/9kts_62564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kts_62564/07_2026/9kts_62564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kts_62564/07_2026/9kts_62564.map" model { file = "/net/cci-nas-00/data/ceres_data/9kts_62564/07_2026/9kts_62564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kts_62564/07_2026/9kts_62564.cif" } resolution = 3.2 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= 0.021 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 32 5.16 5 Cl 1 4.86 5 C 2820 2.51 5 N 644 2.21 5 O 731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4228 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4218 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 27, 'TRANS': 509} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 9 Ad-hoc single atom residues: {' CL': 1} Classifications: {'water': 9} Link IDs: {None: 8} Chain breaks: 1 Time building chain proxies: 1.20, per 1000 atoms: 0.28 Number of scatterers: 4228 At special positions: 0 Unit cell: (82.41, 69.68, 81.74, 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) Cl 1 17.00 S 32 16.00 O 731 8.00 N 644 7.00 C 2820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 151.8 milliseconds 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.3% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.504A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.406A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 152 removed outlier: 3.841A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.403A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 236 Processing helix chain 'A' and resid 244 through 267 removed outlier: 3.785A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.878A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 303 removed outlier: 4.195A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.718A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.015A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.758A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.667A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 removed outlier: 4.093A pdb=" N PHE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.102A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.914A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.512A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.402A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.658A pdb=" N PHE A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.921A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 272 hydrogen bonds defined for protein. 795 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: 0.62 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1239 1.35 - 1.46: 1241 1.46 - 1.58: 1829 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 4355 Sorted by residual: bond pdb=" C VAL A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.87e+00 bond pdb=" CA VAL A 239 " pdb=" CB VAL A 239 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.26e-01 bond pdb=" C PHE A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.36e-02 5.41e+03 3.20e-01 bond pdb=" CA THR A 242 " pdb=" CB THR A 242 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.86e-02 2.89e+03 2.79e-01 bond pdb=" N TYR A 418 " pdb=" CA TYR A 418 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.41e-02 5.03e+03 2.70e-01 ... (remaining 4350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 5903 2.05 - 4.10: 36 4.10 - 6.15: 8 6.15 - 8.20: 0 8.20 - 10.26: 1 Bond angle restraints: 5948 Sorted by residual: angle pdb=" C THR A 242 " pdb=" CA THR A 242 " pdb=" CB THR A 242 " ideal model delta sigma weight residual 116.54 110.98 5.56 1.15e+00 7.56e-01 2.34e+01 angle pdb=" CA LEU A 573 " pdb=" CB LEU A 573 " pdb=" CG LEU A 573 " ideal model delta sigma weight residual 116.30 126.56 -10.26 3.50e+00 8.16e-02 8.59e+00 angle pdb=" CA THR A 242 " pdb=" C THR A 242 " pdb=" N GLY A 243 " ideal model delta sigma weight residual 119.52 117.27 2.25 7.90e-01 1.60e+00 8.11e+00 angle pdb=" C ASN A 533 " pdb=" N LYS A 534 " pdb=" CA LYS A 534 " ideal model delta sigma weight residual 122.08 125.34 -3.26 1.47e+00 4.63e-01 4.93e+00 angle pdb=" CA TRP A 470 " pdb=" CB TRP A 470 " pdb=" CG TRP A 470 " ideal model delta sigma weight residual 113.60 116.74 -3.14 1.90e+00 2.77e-01 2.74e+00 ... (remaining 5943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2351 16.15 - 32.29: 90 32.29 - 48.43: 9 48.43 - 64.58: 4 64.58 - 80.72: 1 Dihedral angle restraints: 2455 sinusoidal: 910 harmonic: 1545 Sorted by residual: dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta harmonic sigma weight residual 180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" N TYR A 69 " pdb=" CA TYR A 69 " pdb=" CB TYR A 69 " pdb=" CG TYR A 69 " ideal model delta sinusoidal sigma weight residual 60.00 116.35 -56.35 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" N LEU A 395 " pdb=" CA LEU A 395 " pdb=" CB LEU A 395 " pdb=" CG LEU A 395 " ideal model delta sinusoidal sigma weight residual -180.00 -125.44 -54.56 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 2452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 436 0.032 - 0.064: 166 0.064 - 0.096: 38 0.096 - 0.128: 18 0.128 - 0.161: 1 Chirality restraints: 659 Sorted by residual: chirality pdb=" CG LEU A 573 " pdb=" CB LEU A 573 " pdb=" CD1 LEU A 573 " pdb=" CD2 LEU A 573 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL A 528 " pdb=" N VAL A 528 " pdb=" C VAL A 528 " pdb=" CB VAL A 528 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA THR A 512 " pdb=" N THR A 512 " pdb=" C THR A 512 " pdb=" CB THR A 512 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 656 not shown) Planarity restraints: 729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 93 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO A 208 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 144 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C TRP A 144 " 0.018 2.00e-02 2.50e+03 pdb=" O TRP A 144 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA A 145 " -0.006 2.00e-02 2.50e+03 ... (remaining 726 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1124 2.80 - 3.33: 4311 3.33 - 3.85: 7244 3.85 - 4.38: 8368 4.38 - 4.90: 14714 Nonbonded interactions: 35761 Sorted by model distance: nonbonded pdb=" O SER A 311 " pdb=" OG SER A 314 " model vdw 2.278 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.280 3.120 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.324 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OD1 ASN A 333 " model vdw 2.336 3.120 nonbonded pdb=" NE2 GLN A 289 " pdb=" OD1 ASP A 293 " model vdw 2.352 3.120 ... (remaining 35756 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: 5.000 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.820 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 0.019 4356 Z= 0.096 Angle : 0.459 10.256 5950 Z= 0.249 Chirality : 0.038 0.161 659 Planarity : 0.003 0.027 729 Dihedral : 9.071 80.723 1474 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.25 % Allowed : 3.37 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.38), residues: 533 helix: 1.11 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.94 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 575 TYR 0.012 0.001 TYR A 69 PHE 0.010 0.001 PHE A 386 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.10 ( 4355) covalent geometry : angle 0.45893 / 0.25 ( 5948) SS BOND : bond 0.00285 / 0.15 ( 1) SS BOND : angle 1.02004 / 0.60 ( 2) hydrogen bonds : bond 0.16923 / 12.04 ( 272) hydrogen bonds : angle 7.47981 / 5.17 ( 795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.151 Fit side-chains REVERT: A 233 PHE cc_start: 0.6535 (m-10) cc_final: 0.6165 (m-80) REVERT: A 359 ILE cc_start: 0.8507 (mt) cc_final: 0.8268 (mt) REVERT: A 395 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8434 (mp) outliers start: 10 outliers final: 2 residues processed: 96 average time/residue: 0.0677 time to fit residues: 8.3120 Evaluate side-chains 67 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS A 212 HIS A 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.145942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.127979 restraints weight = 4995.429| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.66 r_work: 0.3242 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4356 Z= 0.140 Angle : 0.497 6.066 5950 Z= 0.260 Chirality : 0.040 0.137 659 Planarity : 0.004 0.034 729 Dihedral : 4.886 57.229 587 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.25 % Allowed : 8.54 % Favored : 89.21 % 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: 1.11 (0.37), residues: 533 helix: 1.46 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.08 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 427 TYR 0.018 0.001 TYR A 69 PHE 0.023 0.001 PHE A 404 TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4355) covalent geometry : angle 0.49583 / 0.26 ( 5948) SS BOND : bond 0.00466 / 0.25 ( 1) SS BOND : angle 1.95415 / 1.11 ( 2) hydrogen bonds : bond 0.04194 / 2.81 ( 272) hydrogen bonds : angle 4.99447 / 3.48 ( 795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.098 Fit side-chains REVERT: A 207 SER cc_start: 0.8610 (m) cc_final: 0.8082 (p) REVERT: A 233 PHE cc_start: 0.6906 (m-10) cc_final: 0.6610 (m-80) REVERT: A 258 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8404 (tt) REVERT: A 328 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.6725 (mp) REVERT: A 359 ILE cc_start: 0.8561 (mt) cc_final: 0.8244 (mt) REVERT: A 581 THR cc_start: 0.8296 (m) cc_final: 0.8033 (p) outliers start: 10 outliers final: 5 residues processed: 78 average time/residue: 0.0607 time to fit residues: 6.2033 Evaluate side-chains 69 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.143638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.126003 restraints weight = 4965.274| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.56 r_work: 0.3228 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4356 Z= 0.149 Angle : 0.506 6.444 5950 Z= 0.262 Chirality : 0.041 0.130 659 Planarity : 0.004 0.033 729 Dihedral : 4.613 54.384 585 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.82 % Allowed : 8.76 % Favored : 87.42 % 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: 1.17 (0.37), residues: 533 helix: 1.49 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.96 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 499 TYR 0.019 0.001 TYR A 69 PHE 0.017 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 4355) covalent geometry : angle 0.50498 / 0.26 ( 5948) SS BOND : bond 0.00449 / 0.24 ( 1) SS BOND : angle 1.76284 / 1.00 ( 2) hydrogen bonds : bond 0.04030 / 2.72 ( 272) hydrogen bonds : angle 4.72060 / 3.30 ( 795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 207 SER cc_start: 0.8590 (m) cc_final: 0.8064 (p) REVERT: A 328 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.6827 (mp) REVERT: A 359 ILE cc_start: 0.8560 (mt) cc_final: 0.8262 (mt) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.0470 time to fit residues: 5.3317 Evaluate side-chains 77 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124145 restraints weight = 4985.940| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.56 r_work: 0.3198 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4356 Z= 0.172 Angle : 0.527 7.176 5950 Z= 0.273 Chirality : 0.042 0.132 659 Planarity : 0.004 0.035 729 Dihedral : 4.758 54.375 585 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.04 % Allowed : 9.44 % Favored : 86.52 % 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: 1.00 (0.37), residues: 533 helix: 1.38 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.09 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 428 TYR 0.019 0.001 TYR A 69 PHE 0.018 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 4355) covalent geometry : angle 0.52647 / 0.27 ( 5948) SS BOND : bond 0.00498 / 0.26 ( 1) SS BOND : angle 1.83386 / 1.04 ( 2) hydrogen bonds : bond 0.04113 / 2.79 ( 272) hydrogen bonds : angle 4.75220 / 3.33 ( 795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.114 Fit side-chains REVERT: A 207 SER cc_start: 0.8583 (m) cc_final: 0.8056 (p) REVERT: A 258 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8454 (tt) REVERT: A 328 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.6860 (mp) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.0531 time to fit residues: 5.3235 Evaluate side-chains 77 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.145662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.128344 restraints weight = 4953.000| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.57 r_work: 0.3247 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4356 Z= 0.151 Angle : 0.506 7.483 5950 Z= 0.262 Chirality : 0.041 0.130 659 Planarity : 0.004 0.035 729 Dihedral : 4.712 53.866 585 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.04 % Allowed : 8.99 % Favored : 86.97 % 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: 1.06 (0.37), residues: 533 helix: 1.46 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.13 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 564 TYR 0.019 0.001 TYR A 69 PHE 0.017 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 4355) covalent geometry : angle 0.50549 / 0.26 ( 5948) SS BOND : bond 0.00460 / 0.24 ( 1) SS BOND : angle 1.71524 / 0.97 ( 2) hydrogen bonds : bond 0.03913 / 2.66 ( 272) hydrogen bonds : angle 4.67025 / 3.28 ( 795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.151 Fit side-chains REVERT: A 207 SER cc_start: 0.8584 (m) cc_final: 0.8055 (p) REVERT: A 258 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8478 (tt) REVERT: A 328 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.6840 (mp) outliers start: 18 outliers final: 14 residues processed: 80 average time/residue: 0.0491 time to fit residues: 5.3553 Evaluate side-chains 77 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.140785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.123635 restraints weight = 5128.351| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.54 r_work: 0.3279 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4356 Z= 0.155 Angle : 0.512 7.173 5950 Z= 0.265 Chirality : 0.041 0.129 659 Planarity : 0.004 0.035 729 Dihedral : 4.760 53.981 585 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.27 % Allowed : 8.99 % Favored : 86.74 % 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: 1.02 (0.37), residues: 533 helix: 1.43 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.16 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 564 TYR 0.019 0.001 TYR A 69 PHE 0.017 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 4355) covalent geometry : angle 0.51075 / 0.26 ( 5948) SS BOND : bond 0.00445 / 0.23 ( 1) SS BOND : angle 1.68098 / 0.95 ( 2) hydrogen bonds : bond 0.03963 / 2.69 ( 272) hydrogen bonds : angle 4.65059 / 3.26 ( 795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.151 Fit side-chains REVERT: A 207 SER cc_start: 0.8555 (m) cc_final: 0.8041 (p) REVERT: A 258 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 328 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.6959 (mp) REVERT: A 395 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8523 (mp) outliers start: 19 outliers final: 16 residues processed: 75 average time/residue: 0.0526 time to fit residues: 5.3920 Evaluate side-chains 78 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.141865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.124527 restraints weight = 5086.902| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.57 r_work: 0.3314 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4356 Z= 0.135 Angle : 0.497 7.200 5950 Z= 0.257 Chirality : 0.040 0.127 659 Planarity : 0.004 0.035 729 Dihedral : 4.693 53.971 585 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.49 % Allowed : 8.99 % Favored : 86.52 % 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: 1.10 (0.37), residues: 533 helix: 1.50 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.13 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 564 TYR 0.018 0.001 TYR A 69 PHE 0.015 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4355) covalent geometry : angle 0.49632 / 0.26 ( 5948) SS BOND : bond 0.00406 / 0.21 ( 1) SS BOND : angle 1.65423 / 0.94 ( 2) hydrogen bonds : bond 0.03777 / 2.57 ( 272) hydrogen bonds : angle 4.57491 / 3.21 ( 795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.091 Fit side-chains REVERT: A 207 SER cc_start: 0.8552 (m) cc_final: 0.8037 (p) REVERT: A 258 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8535 (tt) REVERT: A 328 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.6999 (mp) REVERT: A 395 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8515 (mp) outliers start: 20 outliers final: 16 residues processed: 79 average time/residue: 0.0504 time to fit residues: 5.2252 Evaluate side-chains 80 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.141511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.124480 restraints weight = 4993.441| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.52 r_work: 0.3211 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4356 Z= 0.149 Angle : 0.511 6.846 5950 Z= 0.265 Chirality : 0.041 0.129 659 Planarity : 0.004 0.035 729 Dihedral : 4.748 53.953 585 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.27 % Allowed : 9.21 % Favored : 86.52 % 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: 1.03 (0.37), residues: 533 helix: 1.46 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.22 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 201 TYR 0.018 0.001 TYR A 69 PHE 0.017 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 4355) covalent geometry : angle 0.51047 / 0.27 ( 5948) SS BOND : bond 0.00412 / 0.22 ( 1) SS BOND : angle 1.63298 / 0.93 ( 2) hydrogen bonds : bond 0.03856 / 2.62 ( 272) hydrogen bonds : angle 4.59701 / 3.23 ( 795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.091 Fit side-chains REVERT: A 207 SER cc_start: 0.8567 (m) cc_final: 0.8053 (p) REVERT: A 258 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 328 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.6941 (mp) REVERT: A 395 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8497 (mp) outliers start: 19 outliers final: 16 residues processed: 75 average time/residue: 0.0568 time to fit residues: 5.7427 Evaluate side-chains 78 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.141237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.123979 restraints weight = 5102.572| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.56 r_work: 0.3202 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4356 Z= 0.144 Angle : 0.510 6.892 5950 Z= 0.264 Chirality : 0.040 0.127 659 Planarity : 0.004 0.035 729 Dihedral : 4.737 53.943 585 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.27 % Allowed : 9.21 % Favored : 86.52 % 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: 1.05 (0.37), residues: 533 helix: 1.49 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.24 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.018 0.001 TYR A 69 PHE 0.016 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 4355) covalent geometry : angle 0.50892 / 0.26 ( 5948) SS BOND : bond 0.00445 / 0.23 ( 1) SS BOND : angle 1.68675 / 0.96 ( 2) hydrogen bonds : bond 0.03820 / 2.59 ( 272) hydrogen bonds : angle 4.58054 / 3.21 ( 795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.110 Fit side-chains REVERT: A 207 SER cc_start: 0.8586 (m) cc_final: 0.8066 (p) REVERT: A 258 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8430 (tt) REVERT: A 328 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.6899 (mp) REVERT: A 395 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8470 (mp) outliers start: 19 outliers final: 16 residues processed: 76 average time/residue: 0.0514 time to fit residues: 5.2829 Evaluate side-chains 79 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.140124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123057 restraints weight = 5009.181| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.51 r_work: 0.3200 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4356 Z= 0.160 Angle : 0.527 6.963 5950 Z= 0.274 Chirality : 0.041 0.130 659 Planarity : 0.004 0.036 729 Dihedral : 4.806 53.838 585 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.04 % Allowed : 9.66 % Favored : 86.29 % 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: 0.97 (0.37), residues: 533 helix: 1.42 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.27 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.019 0.001 TYR A 69 PHE 0.018 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 4355) covalent geometry : angle 0.52605 / 0.27 ( 5948) SS BOND : bond 0.00469 / 0.25 ( 1) SS BOND : angle 1.65196 / 0.94 ( 2) hydrogen bonds : bond 0.03969 / 2.70 ( 272) hydrogen bonds : angle 4.63457 / 3.26 ( 795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.156 Fit side-chains REVERT: A 207 SER cc_start: 0.8573 (m) cc_final: 0.8045 (p) REVERT: A 258 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8445 (tt) REVERT: A 328 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.6985 (mp) REVERT: A 575 ARG cc_start: 0.7458 (mtm180) cc_final: 0.7097 (mtm180) outliers start: 18 outliers final: 16 residues processed: 75 average time/residue: 0.0575 time to fit residues: 5.8192 Evaluate side-chains 77 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.142508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.125064 restraints weight = 5059.217| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.61 r_work: 0.3217 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4356 Z= 0.158 Angle : 0.524 6.699 5950 Z= 0.273 Chirality : 0.041 0.129 659 Planarity : 0.004 0.036 729 Dihedral : 4.796 53.803 585 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.27 % Allowed : 9.44 % Favored : 86.29 % 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: 1.05 (0.37), residues: 533 helix: 1.49 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.18 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.019 0.001 TYR A 69 PHE 0.017 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 4355) covalent geometry : angle 0.52287 / 0.27 ( 5948) SS BOND : bond 0.00478 / 0.25 ( 1) SS BOND : angle 1.64736 / 0.93 ( 2) hydrogen bonds : bond 0.03939 / 2.67 ( 272) hydrogen bonds : angle 4.63505 / 3.25 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1116.33 seconds wall clock time: 19 minutes 51.01 seconds (1191.01 seconds total)