Starting phenix.real_space_refine on Thu Mar 6 07:14:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgg_31968/03_2025/7vgg_31968.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgg_31968/03_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_31968/03_2025/7vgg_31968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgg_31968/03_2025/7vgg_31968.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgg_31968/03_2025/7vgg_31968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgg_31968/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.57, per 1000 atoms: 0.68 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: 1.10 Conformation dependent library (CDL) restraints added in 599.9 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: 0.67 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: 1.77 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.450 ------------------------------------------------------------------------------- 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 : 0.570 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: 0.1892 time to fit residues: 18.0342 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 : 0.630 ------------------------------------------------------------------------------- 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 = 0.142694 restraints weight = 6088.114| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.01 r_work: 0.3585 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- 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 : 0.624 Fit side-chains REVERT: A 467 TRP cc_start: 0.8860 (m100) cc_final: 0.8643 (m100) REVERT: B 175 LYS cc_start: 0.8233 (tttt) cc_final: 0.7382 (tptp) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.1908 time to fit residues: 16.9425 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 : 0.605 ------------------------------------------------------------------------------- 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: 0.7980 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 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: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.167154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142127 restraints weight = 6141.582| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.05 r_work: 0.3568 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1615 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= 0.204 Angle : 0.492 4.501 7311 Z= 0.268 Chirality : 0.047 0.151 793 Planarity : 0.004 0.043 944 Dihedral : 4.300 18.396 733 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.92 % Allowed : 9.27 % Favored : 88.81 % 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: -0.44 (0.33), residues: 668 helix: 2.31 (2.76), residues: 7 sheet: -0.64 (0.32), residues: 239 loop : -0.02 (0.32), 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 0.004 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 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.582 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.1896 time to fit residues: 17.1019 Evaluate side-chains 62 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 228 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.162685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136771 restraints weight = 6313.117| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.10 r_work: 0.3494 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5394 Z= 0.378 Angle : 0.582 8.075 7311 Z= 0.311 Chirality : 0.050 0.163 793 Planarity : 0.004 0.045 944 Dihedral : 4.603 18.749 733 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.10 % Allowed : 11.19 % Favored : 86.71 % 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: -0.73 (0.32), residues: 668 helix: 2.39 (2.70), residues: 7 sheet: -0.86 (0.32), residues: 239 loop : -0.21 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 250 HIS 0.011 0.002 HIS A 543 PHE 0.012 0.002 PHE A 386 TYR 0.019 0.002 TYR A 617 ARG 0.003 0.001 ARG B 338 *********************** 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 67 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.620 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.1562 time to fit residues: 12.9659 Evaluate side-chains 60 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 0.0170 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.167482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142579 restraints weight = 6158.198| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.01 r_work: 0.3603 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.003 0.021 5394 Z= 0.169 Angle : 0.476 4.856 7311 Z= 0.262 Chirality : 0.046 0.151 793 Planarity : 0.003 0.045 944 Dihedral : 4.239 16.723 733 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.92 % Allowed : 12.59 % Favored : 85.49 % 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: -0.71 (0.32), residues: 668 helix: 2.69 (2.54), residues: 7 sheet: -0.80 (0.32), residues: 231 loop : -0.25 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 198 HIS 0.004 0.001 HIS A 543 PHE 0.012 0.001 PHE A 398 TYR 0.019 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 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.472 Fit side-chains REVERT: B 228 MET cc_start: 0.8310 (mtp) cc_final: 0.8101 (ptp) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.1660 time to fit residues: 15.4212 Evaluate side-chains 63 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 414 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 577 VAL 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 23 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN B 142 GLN B 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.163762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138287 restraints weight = 6299.901| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.01 r_work: 0.3506 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 5394 Z= 0.539 Angle : 0.666 8.832 7311 Z= 0.355 Chirality : 0.053 0.161 793 Planarity : 0.005 0.053 944 Dihedral : 4.944 20.244 733 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.62 % Allowed : 12.59 % Favored : 84.79 % 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: -0.95 (0.32), residues: 668 helix: 2.14 (2.41), residues: 7 sheet: -0.98 (0.32), residues: 226 loop : -0.41 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 250 HIS 0.014 0.002 HIS A 543 PHE 0.018 0.003 PHE B 305 TYR 0.020 0.002 TYR A 617 ARG 0.010 0.001 ARG B 338 *********************** 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 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.548 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 62 average time/residue: 0.1681 time to fit residues: 14.2601 Evaluate side-chains 64 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141164 restraints weight = 6168.736| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.00 r_work: 0.3591 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2174 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= 0.186 Angle : 0.498 6.289 7311 Z= 0.274 Chirality : 0.047 0.167 793 Planarity : 0.003 0.047 944 Dihedral : 4.424 17.110 733 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.10 % Allowed : 13.64 % 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 (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: -0.85 (0.32), residues: 668 helix: 2.80 (2.51), residues: 7 sheet: -1.03 (0.31), residues: 236 loop : -0.24 (0.31), residues: 425 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 0.012 0.001 PHE A 398 TYR 0.018 0.001 TYR A 617 ARG 0.007 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 71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.603 Fit side-chains REVERT: A 593 LYS cc_start: 0.8022 (pttp) cc_final: 0.7794 (ptmt) REVERT: B 228 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7959 (ptp) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.1577 time to fit residues: 14.1451 Evaluate side-chains 63 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.164258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138871 restraints weight = 6272.800| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.03 r_work: 0.3553 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5394 Z= 0.307 Angle : 0.550 6.721 7311 Z= 0.300 Chirality : 0.049 0.162 793 Planarity : 0.004 0.048 944 Dihedral : 4.543 17.989 733 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.80 % Allowed : 13.81 % 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: -0.86 (0.32), residues: 668 helix: 2.68 (2.50), residues: 7 sheet: -1.02 (0.32), residues: 234 loop : -0.27 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 198 HIS 0.008 0.001 HIS A 543 PHE 0.018 0.002 PHE A 595 TYR 0.020 0.002 TYR A 617 ARG 0.010 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 72 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.608 Fit side-chains REVERT: A 593 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7758 (ptmt) outliers start: 16 outliers final: 11 residues processed: 61 average time/residue: 0.1724 time to fit residues: 14.1806 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 : 0.530 ------------------------------------------------------------------------------- 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 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 64 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.165799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140848 restraints weight = 6175.131| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.01 r_work: 0.3553 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5394 Z= 0.220 Angle : 0.517 6.149 7311 Z= 0.285 Chirality : 0.047 0.173 793 Planarity : 0.004 0.048 944 Dihedral : 4.430 17.074 733 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.62 % Allowed : 13.81 % Favored : 83.57 % 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: -0.80 (0.32), residues: 668 helix: 2.75 (2.47), residues: 7 sheet: -0.98 (0.32), residues: 234 loop : -0.23 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 198 HIS 0.006 0.001 HIS A 543 PHE 0.018 0.002 PHE A 595 TYR 0.019 0.001 TYR A 617 ARG 0.004 0.000 ARG B 217 *********************** 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 70 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.555 Fit side-chains REVERT: A 593 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7752 (ptmt) REVERT: B 228 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7946 (ptp) outliers start: 15 outliers final: 10 residues processed: 61 average time/residue: 0.1428 time to fit residues: 12.2961 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 : 0.548 ------------------------------------------------------------------------------- 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 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 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 15 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.166294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141149 restraints weight = 6236.333| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.03 r_work: 0.3577 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5394 Z= 0.200 Angle : 0.503 5.663 7311 Z= 0.277 Chirality : 0.047 0.161 793 Planarity : 0.004 0.048 944 Dihedral : 4.340 16.827 733 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.62 % Allowed : 13.64 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.32), residues: 668 helix: 2.84 (2.42), residues: 7 sheet: -1.00 (0.30), residues: 249 loop : -0.10 (0.32), residues: 412 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 0.016 0.001 PHE A 595 TYR 0.019 0.001 TYR A 617 ARG 0.004 0.000 ARG B 217 ********************** 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 70 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.716 Fit side-chains REVERT: A 593 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7728 (ptmt) REVERT: B 228 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7949 (ptp) outliers start: 15 outliers final: 10 residues processed: 61 average time/residue: 0.2376 time to fit residues: 20.4720 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 : 0.938 ------------------------------------------------------------------------------- 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 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 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 35 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.167190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142148 restraints weight = 6258.432| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.03 r_work: 0.3590 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5394 Z= 0.174 Angle : 0.494 5.673 7311 Z= 0.273 Chirality : 0.046 0.160 793 Planarity : 0.004 0.048 944 Dihedral : 4.231 16.327 733 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.27 % Allowed : 13.64 % 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: -0.67 (0.32), residues: 668 helix: 2.89 (2.38), residues: 7 sheet: -0.96 (0.30), residues: 249 loop : -0.04 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 198 HIS 0.005 0.001 HIS A 543 PHE 0.015 0.001 PHE A 595 TYR 0.018 0.001 TYR A 617 ARG 0.004 0.000 ARG B 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3137.49 seconds wall clock time: 54 minutes 37.67 seconds (3277.67 seconds total)