Starting phenix.real_space_refine on Tue Feb 11 10:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgg_31968/02_2025/7vgg_31968.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgg_31968/02_2025/7vgg_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_31968/02_2025/7vgg_31968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgg_31968/02_2025/7vgg_31968.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgg_31968/02_2025/7vgg_31968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgg_31968/02_2025/7vgg_31968.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.74, per 1000 atoms: 0.71 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: 1.28 Conformation dependent library (CDL) restraints added in 635.9 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: 0.64 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: 1.99 Time building geometry restraints manager: 1.43 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: 1.550 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.180 ------------------------------------------------------------------------------- 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= 0.245 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 : 6.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.002 TRP B 302 HIS 0.005 0.001 HIS B 102 PHE 0.013 0.002 PHE A 630 TYR 0.016 0.001 TYR A 441 ARG 0.002 0.000 ARG B 354 *********************** 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 : 0.614 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: 0.1955 time to fit residues: 18.7887 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 : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.167381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.142696 restraints weight = 6088.114| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.00 r_work: 0.3584 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5394 Z= 0.237 Angle : 0.534 5.321 7311 Z= 0.289 Chirality : 0.048 0.146 793 Planarity : 0.004 0.044 944 Dihedral : 4.441 17.575 733 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.57 % Allowed : 5.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.33), residues: 668 helix: -0.79 (1.84), residues: 13 sheet: -0.80 (0.32), residues: 239 loop : -0.02 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 198 HIS 0.004 0.001 HIS B 287 PHE 0.011 0.002 PHE A 398 TYR 0.019 0.002 TYR A 617 ARG 0.006 0.001 ARG A 420 *********************** 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 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.616 Fit side-chains REVERT: A 467 TRP cc_start: 0.8859 (m100) cc_final: 0.8644 (m100) REVERT: B 175 LYS cc_start: 0.8225 (tttt) cc_final: 0.7375 (tptp) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.1902 time to fit residues: 16.9287 Evaluate side-chains 61 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 B residue 228 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.166202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.141032 restraints weight = 6145.579| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.05 r_work: 0.3555 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5394 Z= 0.231 Angle : 0.506 4.735 7311 Z= 0.274 Chirality : 0.047 0.153 793 Planarity : 0.004 0.043 944 Dihedral : 4.358 17.611 733 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.33), residues: 668 helix: 2.33 (2.78), residues: 7 sheet: -0.68 (0.32), residues: 239 loop : -0.03 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 250 HIS 0.004 0.001 HIS B 287 PHE 0.012 0.002 PHE A 398 TYR 0.020 0.002 TYR A 617 ARG 0.004 0.000 ARG A 420 *********************** 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 74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.606 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.1971 time to fit residues: 16.9381 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 : 0.594 ------------------------------------------------------------------------------- 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 45 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.165819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140370 restraints weight = 6284.933| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.07 r_work: 0.3572 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1755 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= 0.244 Angle : 0.503 5.079 7311 Z= 0.274 Chirality : 0.048 0.158 793 Planarity : 0.004 0.045 944 Dihedral : 4.308 17.417 733 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.45 % Allowed : 10.31 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.33), residues: 668 helix: 2.50 (2.64), residues: 7 sheet: -0.70 (0.32), residues: 239 loop : -0.14 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 198 HIS 0.004 0.001 HIS B 287 PHE 0.012 0.002 PHE A 398 TYR 0.020 0.001 TYR A 617 ARG 0.002 0.000 ARG B 217 *********************** 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 74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.630 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 66 average time/residue: 0.1452 time to fit residues: 13.4283 Evaluate side-chains 66 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 228 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.167038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141587 restraints weight = 6153.683| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.07 r_work: 0.3586 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5394 Z= 0.196 Angle : 0.476 5.923 7311 Z= 0.259 Chirality : 0.047 0.151 793 Planarity : 0.003 0.044 944 Dihedral : 4.176 16.701 733 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.27 % Allowed : 12.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.32), residues: 668 helix: 2.73 (2.50), residues: 7 sheet: -0.70 (0.32), residues: 236 loop : -0.18 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 250 HIS 0.008 0.001 HIS A 543 PHE 0.012 0.001 PHE A 398 TYR 0.020 0.001 TYR A 617 ARG 0.002 0.000 ARG B 217 *********************** 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 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.549 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 69 average time/residue: 0.1604 time to fit residues: 15.0763 Evaluate side-chains 64 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 414 ILE 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 110 THR Chi-restraints excluded: chain B residue 228 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 23 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- 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 = 0.164945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139200 restraints weight = 6194.421| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.08 r_work: 0.3523 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5394 Z= 0.275 Angle : 0.516 7.280 7311 Z= 0.277 Chirality : 0.048 0.152 793 Planarity : 0.004 0.045 944 Dihedral : 4.332 17.797 733 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.62 % Allowed : 12.76 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.32), residues: 668 helix: 2.83 (2.50), residues: 7 sheet: -0.79 (0.32), residues: 239 loop : -0.17 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 250 HIS 0.008 0.001 HIS A 543 PHE 0.011 0.002 PHE A 398 TYR 0.019 0.002 TYR A 617 ARG 0.002 0.000 ARG A 573 *********************** 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 72 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.592 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.1629 time to fit residues: 14.2064 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 : 0.585 ------------------------------------------------------------------------------- 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 414 ILE 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 228 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.164698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139367 restraints weight = 6186.426| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.02 r_work: 0.3549 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5394 Z= 0.328 Angle : 0.551 7.824 7311 Z= 0.298 Chirality : 0.049 0.152 793 Planarity : 0.004 0.046 944 Dihedral : 4.484 18.399 733 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.62 % Allowed : 12.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.32), residues: 668 helix: 2.81 (2.54), residues: 7 sheet: -0.88 (0.32), residues: 239 loop : -0.22 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 250 HIS 0.009 0.001 HIS A 543 PHE 0.011 0.002 PHE A 398 TYR 0.020 0.002 TYR A 617 ARG 0.003 0.000 ARG B 338 *********************** 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 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.647 Fit side-chains REVERT: A 593 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7696 (ptmt) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.1500 time to fit residues: 13.4106 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 : 0.597 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.163141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137527 restraints weight = 6274.184| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.04 r_work: 0.3533 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5394 Z= 0.358 Angle : 0.574 7.738 7311 Z= 0.311 Chirality : 0.050 0.154 793 Planarity : 0.004 0.048 944 Dihedral : 4.616 18.892 733 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.97 % Allowed : 12.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.32), residues: 668 helix: 2.78 (2.57), residues: 7 sheet: -0.91 (0.32), residues: 234 loop : -0.29 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 250 HIS 0.009 0.002 HIS A 543 PHE 0.012 0.002 PHE A 386 TYR 0.019 0.002 TYR A 617 ARG 0.004 0.001 ARG B 338 *********************** 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 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.569 Fit side-chains REVERT: A 467 TRP cc_start: 0.9000 (m100) cc_final: 0.8715 (m100) REVERT: A 593 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7734 (ptmt) REVERT: B 19 ILE cc_start: 0.9184 (mm) cc_final: 0.8982 (mm) outliers start: 17 outliers final: 10 residues processed: 63 average time/residue: 0.1464 time to fit residues: 12.9839 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 : 0.671 ------------------------------------------------------------------------------- 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 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.167123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142419 restraints weight = 6202.467| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.99 r_work: 0.3568 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5394 Z= 0.223 Angle : 0.512 6.464 7311 Z= 0.281 Chirality : 0.047 0.155 793 Planarity : 0.004 0.048 944 Dihedral : 4.416 17.684 733 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.32), residues: 668 helix: 2.86 (2.53), residues: 7 sheet: -0.87 (0.32), residues: 234 loop : -0.24 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 198 HIS 0.007 0.001 HIS A 543 PHE 0.012 0.001 PHE A 398 TYR 0.018 0.001 TYR A 617 ARG 0.003 0.000 ARG A 536 *********************** 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 : 0.574 Fit side-chains REVERT: A 593 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7728 (ptmt) outliers start: 16 outliers final: 12 residues processed: 61 average time/residue: 0.1742 time to fit residues: 14.5006 Evaluate side-chains 67 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 414 ILE 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 110 THR 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 15 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 66 optimal weight: 0.0470 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.167790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142616 restraints weight = 6214.056| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.04 r_work: 0.3595 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5394 Z= 0.163 Angle : 0.478 5.455 7311 Z= 0.265 Chirality : 0.046 0.164 793 Planarity : 0.004 0.047 944 Dihedral : 4.202 16.928 733 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.62 % Allowed : 13.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.32), residues: 668 helix: 3.03 (2.39), residues: 7 sheet: -0.77 (0.32), residues: 234 loop : -0.16 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 198 HIS 0.004 0.001 HIS A 543 PHE 0.011 0.001 PHE A 398 TYR 0.017 0.001 TYR A 617 ARG 0.003 0.000 ARG A 536 ********************** 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 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.630 Fit side-chains REVERT: A 593 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7698 (ptmt) REVERT: B 228 MET cc_start: 0.8349 (mtp) cc_final: 0.8020 (ptp) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.1474 time to fit residues: 14.3462 Evaluate side-chains 68 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 31 LEU Chi-restraints excluded: chain B residue 110 THR 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 35 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.165771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140337 restraints weight = 6264.674| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.04 r_work: 0.3568 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5394 Z= 0.258 Angle : 0.532 7.129 7311 Z= 0.291 Chirality : 0.048 0.157 793 Planarity : 0.004 0.047 944 Dihedral : 4.337 17.452 733 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.92 % Allowed : 14.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.32), residues: 668 helix: 3.04 (2.42), residues: 7 sheet: -0.86 (0.32), residues: 234 loop : -0.14 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 198 HIS 0.006 0.001 HIS A 543 PHE 0.010 0.001 PHE A 398 TYR 0.019 0.002 TYR A 617 ARG 0.003 0.000 ARG B 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.17 seconds wall clock time: 54 minutes 4.42 seconds (3244.42 seconds total)