Starting phenix.real_space_refine on Tue Mar 3 13:35:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgg_31968/03_2026/7vgg_31968.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgg_31968/03_2026/7vgg_31968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vgg_31968/03_2026/7vgg_31968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgg_31968/03_2026/7vgg_31968.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgg_31968/03_2026/7vgg_31968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgg_31968/03_2026/7vgg_31968.cif" } resolution = 3.1 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3298 2.51 5 N 940 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2417 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2857 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 12, 'TRANS': 363} Chain breaks: 1 Time building chain proxies: 1.33, per 1000 atoms: 0.25 Number of scatterers: 5274 At special positions: 0 Unit cell: (64.506, 66.16, 91.797, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1010 8.00 N 940 7.00 C 3298 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: 0.44 Conformation dependent library (CDL) restraints added in 323.8 milliseconds 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 4.9% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.946A pdb=" N GLY B 98 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 118 Processing helix chain 'B' and resid 167 through 170 Processing helix chain 'B' and resid 271 through 274 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.548A pdb=" N GLN B 328 " --> pdb=" O PRO B 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 362 removed outlier: 5.102A pdb=" N LEU A 356 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA A 674 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL A 358 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 672 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 360 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 670 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR A 658 " --> pdb=" O TRP A 652 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP A 652 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 660 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 650 " --> pdb=" O LEU A 660 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA A 662 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 374 through 379 removed outlier: 4.458A pdb=" N GLY A 390 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N CYS A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 428 removed outlier: 3.689A pdb=" N CYS A 425 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP A 449 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER A 455 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 471 removed outlier: 3.866A pdb=" N LYS A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS A 492 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER A 498 " --> pdb=" O CYS A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.306A pdb=" N TYR A 520 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 552 through 557 removed outlier: 4.060A pdb=" N THR A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG A 584 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP A 576 " --> pdb=" O PRO A 582 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600 Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 22 removed outlier: 6.443A pdb=" N LEU B 30 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE B 20 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 28 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA B 22 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 36 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B 59 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER B 38 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER B 57 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 74 Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 127 removed outlier: 6.480A pdb=" N VAL B 135 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 125 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 133 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N CYS B 127 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS B 131 " --> pdb=" O CYS B 127 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY B 145 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 162 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.132A pdb=" N GLY B 195 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 214 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 226 through 231 removed outlier: 6.208A pdb=" N THR B 247 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE B 266 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.738A pdb=" N LEU B 297 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLY B 301 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER B 318 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 330 through 335 removed outlier: 6.703A pdb=" N VAL B 349 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS B 372 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA B 351 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B 370 " --> pdb=" O ALA B 351 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 402 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: 0.91 Time building geometry restraints manager: 0.55 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: 1768 1.34 - 1.46: 1118 1.46 - 1.57: 2471 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 5394 Sorted by residual: bond pdb=" C SER B 282 " pdb=" N GLY B 283 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 8.69e-01 bond pdb=" C ARG B 55 " pdb=" O ARG B 55 " ideal model delta sigma weight residual 1.244 1.235 0.008 9.30e-03 1.16e+04 8.00e-01 bond pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta sigma weight residual 1.447 1.437 0.010 1.23e-02 6.61e+03 7.17e-01 bond pdb=" CB ASN B 203 " pdb=" CG ASN B 203 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.09e-01 bond pdb=" CG1 ILE B 174 " pdb=" CD1 ILE B 174 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.88e-01 ... (remaining 5389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 6642 0.90 - 1.79: 544 1.79 - 2.69: 88 2.69 - 3.58: 30 3.58 - 4.48: 7 Bond angle restraints: 7311 Sorted by residual: angle pdb=" CA VAL B 214 " pdb=" C VAL B 214 " pdb=" N PRO B 215 " ideal model delta sigma weight residual 116.57 119.35 -2.78 9.80e-01 1.04e+00 8.07e+00 angle pdb=" N CYS A 651 " pdb=" CA CYS A 651 " pdb=" C CYS A 651 " ideal model delta sigma weight residual 107.93 112.41 -4.48 1.65e+00 3.67e-01 7.37e+00 angle pdb=" CA ARG A 623 " pdb=" C ARG A 623 " pdb=" N PRO A 624 " ideal model delta sigma weight residual 118.23 120.34 -2.11 9.20e-01 1.18e+00 5.26e+00 angle pdb=" N LYS A 512 " pdb=" CA LYS A 512 " pdb=" C LYS A 512 " ideal model delta sigma weight residual 108.48 112.31 -3.83 1.80e+00 3.09e-01 4.54e+00 angle pdb=" N SER A 539 " pdb=" CA SER A 539 " pdb=" C SER A 539 " ideal model delta sigma weight residual 112.12 109.45 2.67 1.34e+00 5.57e-01 3.98e+00 ... (remaining 7306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 2860 16.37 - 32.75: 207 32.75 - 49.12: 59 49.12 - 65.49: 17 65.49 - 81.86: 3 Dihedral angle restraints: 3146 sinusoidal: 1222 harmonic: 1924 Sorted by residual: dihedral pdb=" CA ASP B 211 " pdb=" CB ASP B 211 " pdb=" CG ASP B 211 " pdb=" OD1 ASP B 211 " ideal model delta sinusoidal sigma weight residual -30.00 -89.70 59.70 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA VAL A 600 " pdb=" C VAL A 600 " pdb=" N ASN A 601 " pdb=" CA ASN A 601 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CG ARG B 323 " pdb=" CD ARG B 323 " pdb=" NE ARG B 323 " pdb=" CZ ARG B 323 " ideal model delta sinusoidal sigma weight residual -90.00 -132.10 42.10 2 1.50e+01 4.44e-03 9.59e+00 ... (remaining 3143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 405 0.029 - 0.057: 266 0.057 - 0.086: 47 0.086 - 0.115: 52 0.115 - 0.143: 23 Chirality restraints: 793 Sorted by residual: chirality pdb=" CA ILE A 377 " pdb=" N ILE A 377 " pdb=" C ILE A 377 " pdb=" CB ILE A 377 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE A 395 " pdb=" N ILE A 395 " pdb=" C ILE A 395 " pdb=" CB ILE A 395 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA VAL A 488 " pdb=" N VAL A 488 " pdb=" C VAL A 488 " pdb=" CB VAL A 488 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 790 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 214 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO B 215 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 441 " 0.011 2.00e-02 2.50e+03 7.12e-03 1.01e+00 pdb=" CG TYR A 441 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 441 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 441 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 441 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 441 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 441 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 441 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 367 " 0.004 2.00e-02 2.50e+03 8.79e-03 7.72e-01 pdb=" CG ASP B 367 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASP B 367 " 0.005 2.00e-02 2.50e+03 pdb=" OD2 ASP B 367 " 0.005 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 78 2.60 - 3.18: 4496 3.18 - 3.75: 8230 3.75 - 4.33: 12727 4.33 - 4.90: 21579 Nonbonded interactions: 47110 Sorted by model distance: nonbonded pdb=" O VAL A 374 " pdb=" OG SER A 648 " model vdw 2.025 3.040 nonbonded pdb=" O ARG A 465 " pdb=" OG SER A 483 " model vdw 2.165 3.040 nonbonded pdb=" NH1 ARG A 420 " pdb=" OD2 ASP B 129 " model vdw 2.234 3.120 nonbonded pdb=" NH1 ARG A 584 " pdb=" O LYS A 619 " model vdw 2.241 3.120 nonbonded pdb=" O THR A 585 " pdb=" OG1 THR A 622 " model vdw 2.250 3.040 ... (remaining 47105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.600 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.004 0.029 5394 Z= 0.176 Angle : 0.566 4.478 7311 Z= 0.336 Chirality : 0.046 0.143 793 Planarity : 0.003 0.035 944 Dihedral : 13.319 81.864 1918 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.81 (0.33), residues: 668 helix: -1.15 (1.64), residues: 13 sheet: -1.07 (0.30), residues: 247 loop : -0.02 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.016 0.001 TYR A 441 PHE 0.013 0.002 PHE A 630 TRP 0.012 0.002 TRP B 302 HIS 0.005 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5394) covalent geometry : angle 0.56632 ( 7311) hydrogen bonds : bond 0.15129 ( 156) hydrogen bonds : angle 7.82829 ( 402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.194 Fit side-chains REVERT: A 422 LYS cc_start: 0.8433 (mtmm) cc_final: 0.8220 (mtmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0760 time to fit residues: 7.2870 Evaluate side-chains 58 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS B 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141948 restraints weight = 6250.157| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.05 r_work: 0.3575 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5394 Z= 0.156 Angle : 0.534 5.317 7311 Z= 0.289 Chirality : 0.048 0.147 793 Planarity : 0.004 0.044 944 Dihedral : 4.446 17.585 733 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.92 % Allowed : 4.90 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.61 (0.33), residues: 668 helix: -0.79 (1.84), residues: 13 sheet: -0.80 (0.31), residues: 239 loop : -0.02 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 420 TYR 0.019 0.002 TYR A 617 PHE 0.011 0.002 PHE A 398 TRP 0.013 0.002 TRP B 198 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5394) covalent geometry : angle 0.53407 ( 7311) hydrogen bonds : bond 0.04131 ( 156) hydrogen bonds : angle 6.02208 ( 402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.206 Fit side-chains REVERT: A 467 TRP cc_start: 0.8866 (m100) cc_final: 0.8646 (m100) REVERT: B 175 LYS cc_start: 0.8231 (tttt) cc_final: 0.7376 (tptp) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 0.0772 time to fit residues: 7.0481 Evaluate side-chains 61 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 228 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.167437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142266 restraints weight = 6198.873| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.08 r_work: 0.3547 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5394 Z= 0.162 Angle : 0.514 4.996 7311 Z= 0.278 Chirality : 0.048 0.154 793 Planarity : 0.004 0.044 944 Dihedral : 4.399 18.382 733 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.10 % Allowed : 9.44 % Favored : 88.46 % 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: -0.50 (0.33), residues: 668 helix: 2.37 (2.82), residues: 7 sheet: -0.70 (0.32), residues: 239 loop : -0.04 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.020 0.002 TYR A 617 PHE 0.012 0.002 PHE A 398 TRP 0.012 0.002 TRP B 198 HIS 0.004 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 5394) covalent geometry : angle 0.51367 ( 7311) hydrogen bonds : bond 0.04024 ( 156) hydrogen bonds : angle 5.69573 ( 402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.203 Fit side-chains REVERT: B 175 LYS cc_start: 0.8220 (tttt) cc_final: 0.8011 (ttmt) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.0722 time to fit residues: 6.0025 Evaluate side-chains 63 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 228 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.161228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135507 restraints weight = 6202.960| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.04 r_work: 0.3481 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5394 Z= 0.290 Angle : 0.616 6.949 7311 Z= 0.329 Chirality : 0.051 0.161 793 Planarity : 0.004 0.046 944 Dihedral : 4.771 19.385 733 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.45 % Allowed : 11.01 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.32), residues: 668 helix: 2.26 (2.67), residues: 7 sheet: -0.91 (0.32), residues: 237 loop : -0.26 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 573 TYR 0.020 0.002 TYR A 617 PHE 0.013 0.002 PHE A 386 TRP 0.016 0.003 TRP B 250 HIS 0.007 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00665 ( 5394) covalent geometry : angle 0.61553 ( 7311) hydrogen bonds : bond 0.04551 ( 156) hydrogen bonds : angle 5.91275 ( 402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.165 Fit side-chains REVERT: A 442 GLU cc_start: 0.8370 (pm20) cc_final: 0.8167 (pm20) REVERT: B 175 LYS cc_start: 0.8235 (tttt) cc_final: 0.7890 (ttmm) outliers start: 14 outliers final: 11 residues processed: 62 average time/residue: 0.0653 time to fit residues: 5.5642 Evaluate side-chains 65 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140487 restraints weight = 6249.957| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.02 r_work: 0.3545 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5394 Z= 0.140 Angle : 0.497 4.827 7311 Z= 0.273 Chirality : 0.047 0.155 793 Planarity : 0.004 0.046 944 Dihedral : 4.425 17.558 733 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.27 % Allowed : 12.06 % Favored : 85.66 % 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: -0.78 (0.32), residues: 668 helix: 2.71 (2.60), residues: 7 sheet: -0.93 (0.31), residues: 241 loop : -0.22 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 217 TYR 0.020 0.001 TYR A 617 PHE 0.012 0.001 PHE A 398 TRP 0.013 0.002 TRP B 198 HIS 0.004 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5394) covalent geometry : angle 0.49743 ( 7311) hydrogen bonds : bond 0.03785 ( 156) hydrogen bonds : angle 5.61245 ( 402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.209 Fit side-chains REVERT: A 467 TRP cc_start: 0.8910 (m100) cc_final: 0.8677 (m100) REVERT: B 175 LYS cc_start: 0.8195 (tttt) cc_final: 0.7785 (ttmm) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.0693 time to fit residues: 6.6516 Evaluate side-chains 66 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 42 optimal weight: 5.9990 chunk 9 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139669 restraints weight = 6280.885| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.05 r_work: 0.3562 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5394 Z= 0.176 Angle : 0.519 6.680 7311 Z= 0.283 Chirality : 0.048 0.155 793 Planarity : 0.004 0.045 944 Dihedral : 4.426 17.767 733 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.62 % Allowed : 12.41 % Favored : 84.97 % 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: -0.78 (0.32), residues: 668 helix: 2.73 (2.52), residues: 7 sheet: -0.97 (0.31), residues: 241 loop : -0.19 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 338 TYR 0.019 0.002 TYR A 617 PHE 0.011 0.002 PHE A 398 TRP 0.012 0.002 TRP B 250 HIS 0.007 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 5394) covalent geometry : angle 0.51930 ( 7311) hydrogen bonds : bond 0.03846 ( 156) hydrogen bonds : angle 5.57939 ( 402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.131 Fit side-chains REVERT: A 467 TRP cc_start: 0.8935 (m100) cc_final: 0.8709 (m100) REVERT: A 593 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7785 (ptmm) REVERT: B 175 LYS cc_start: 0.8212 (tttt) cc_final: 0.7813 (ttmm) outliers start: 15 outliers final: 10 residues processed: 67 average time/residue: 0.0695 time to fit residues: 6.2046 Evaluate side-chains 67 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 228 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.163941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138356 restraints weight = 6310.532| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.07 r_work: 0.3480 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5394 Z= 0.254 Angle : 0.587 7.595 7311 Z= 0.318 Chirality : 0.050 0.163 793 Planarity : 0.004 0.047 944 Dihedral : 4.728 19.080 733 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.15 % Allowed : 12.41 % Favored : 84.44 % 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: -0.85 (0.32), residues: 668 helix: 2.59 (2.51), residues: 7 sheet: -1.00 (0.32), residues: 238 loop : -0.26 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 338 TYR 0.021 0.002 TYR A 617 PHE 0.012 0.002 PHE A 386 TRP 0.015 0.002 TRP B 250 HIS 0.011 0.002 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 5394) covalent geometry : angle 0.58740 ( 7311) hydrogen bonds : bond 0.04209 ( 156) hydrogen bonds : angle 5.79299 ( 402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.216 Fit side-chains REVERT: A 467 TRP cc_start: 0.9026 (m100) cc_final: 0.8802 (m100) REVERT: A 593 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7801 (ptmt) REVERT: B 19 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8964 (mm) REVERT: B 175 LYS cc_start: 0.8260 (tttt) cc_final: 0.7888 (ttmm) outliers start: 18 outliers final: 10 residues processed: 61 average time/residue: 0.0675 time to fit residues: 5.7013 Evaluate side-chains 65 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 228 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140744 restraints weight = 6179.223| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.03 r_work: 0.3539 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5394 Z= 0.138 Angle : 0.491 5.532 7311 Z= 0.272 Chirality : 0.047 0.153 793 Planarity : 0.004 0.048 944 Dihedral : 4.369 17.279 733 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.62 % Allowed : 13.11 % Favored : 84.27 % 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: -0.77 (0.32), residues: 668 helix: 2.83 (2.49), residues: 7 sheet: -0.94 (0.32), residues: 234 loop : -0.22 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 200 TYR 0.018 0.001 TYR A 617 PHE 0.012 0.001 PHE A 398 TRP 0.019 0.002 TRP B 198 HIS 0.005 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5394) covalent geometry : angle 0.49143 ( 7311) hydrogen bonds : bond 0.03564 ( 156) hydrogen bonds : angle 5.50458 ( 402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.218 Fit side-chains REVERT: A 467 TRP cc_start: 0.8933 (m100) cc_final: 0.8681 (m100) REVERT: A 593 LYS cc_start: 0.8195 (pttp) cc_final: 0.7767 (ptmt) REVERT: B 19 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.9013 (mm) REVERT: B 175 LYS cc_start: 0.8227 (tttt) cc_final: 0.7810 (ttmm) REVERT: B 228 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8035 (ptp) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.0803 time to fit residues: 6.9380 Evaluate side-chains 69 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.164138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138830 restraints weight = 6300.399| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.02 r_work: 0.3559 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5394 Z= 0.193 Angle : 0.538 5.806 7311 Z= 0.295 Chirality : 0.049 0.163 793 Planarity : 0.004 0.048 944 Dihedral : 4.477 17.994 733 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.80 % Allowed : 13.29 % Favored : 83.92 % 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: -0.77 (0.32), residues: 668 helix: 2.69 (2.49), residues: 7 sheet: -0.94 (0.32), residues: 233 loop : -0.22 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.021 0.002 TYR A 617 PHE 0.011 0.002 PHE A 398 TRP 0.019 0.002 TRP B 198 HIS 0.008 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 5394) covalent geometry : angle 0.53797 ( 7311) hydrogen bonds : bond 0.03835 ( 156) hydrogen bonds : angle 5.56187 ( 402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.238 Fit side-chains REVERT: A 593 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7827 (ptmt) REVERT: B 19 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.9026 (mm) REVERT: B 146 ARG cc_start: 0.7930 (ptp-170) cc_final: 0.7422 (mtm180) REVERT: B 175 LYS cc_start: 0.8241 (tttt) cc_final: 0.7832 (ttmm) outliers start: 16 outliers final: 12 residues processed: 61 average time/residue: 0.0676 time to fit residues: 5.5901 Evaluate side-chains 68 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 409 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.166909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.141651 restraints weight = 6290.925| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.05 r_work: 0.3585 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5394 Z= 0.117 Angle : 0.488 5.605 7311 Z= 0.271 Chirality : 0.047 0.171 793 Planarity : 0.004 0.048 944 Dihedral : 4.277 16.593 733 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.10 % Allowed : 13.81 % Favored : 84.09 % 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: -0.69 (0.32), residues: 668 helix: 2.92 (2.41), residues: 7 sheet: -0.93 (0.32), residues: 234 loop : -0.13 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.019 0.001 TYR A 617 PHE 0.011 0.001 PHE A 398 TRP 0.018 0.002 TRP B 198 HIS 0.004 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 5394) covalent geometry : angle 0.48778 ( 7311) hydrogen bonds : bond 0.03443 ( 156) hydrogen bonds : angle 5.41077 ( 402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.234 Fit side-chains REVERT: A 467 TRP cc_start: 0.8898 (m100) cc_final: 0.8603 (m100) REVERT: A 593 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7756 (ptmt) REVERT: B 19 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8981 (mm) REVERT: B 175 LYS cc_start: 0.8229 (tttt) cc_final: 0.7822 (ttmm) REVERT: B 228 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8000 (ptp) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.0709 time to fit residues: 6.0814 Evaluate side-chains 66 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 409 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 HIS A 537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.164833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139394 restraints weight = 6286.026| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.05 r_work: 0.3561 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5394 Z= 0.166 Angle : 0.532 7.053 7311 Z= 0.292 Chirality : 0.048 0.158 793 Planarity : 0.004 0.048 944 Dihedral : 4.374 17.461 733 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.62 % Allowed : 13.99 % Favored : 83.39 % 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: -0.73 (0.32), residues: 668 helix: 2.84 (2.43), residues: 7 sheet: -0.99 (0.31), residues: 234 loop : -0.13 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.019 0.002 TYR A 617 PHE 0.010 0.002 PHE A 398 TRP 0.019 0.002 TRP B 198 HIS 0.007 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5394) covalent geometry : angle 0.53154 ( 7311) hydrogen bonds : bond 0.03692 ( 156) hydrogen bonds : angle 5.44707 ( 402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.78 seconds wall clock time: 25 minutes 38.96 seconds (1538.96 seconds total)