Starting phenix.real_space_refine on Mon Mar 11 18:59:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/03_2024/8g0l_29657_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/03_2024/8g0l_29657.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/03_2024/8g0l_29657_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/03_2024/8g0l_29657_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/03_2024/8g0l_29657_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/03_2024/8g0l_29657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/03_2024/8g0l_29657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/03_2024/8g0l_29657_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0l_29657/03_2024/8g0l_29657_updated.pdb" } resolution = 3.39 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 48 5.16 5 C 5674 2.51 5 N 1487 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1274 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "B" Number of atoms: 7531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7531 Classifications: {'peptide': 925} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 891} Chain breaks: 4 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 67 Unusual residues: {'CMC': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="MET C 5 " pdbres="CMC C 201 " Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CMC:plan-5': 1, 'CMC:plan-3': 1, 'CMC:plan-1': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 5.26, per 1000 atoms: 0.59 Number of scatterers: 8872 At special positions: 0 Unit cell: (77.4, 111.8, 127.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 1 15.00 O 1662 8.00 N 1487 7.00 C 5674 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.8 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 3 sheets defined 67.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 16 through 19 No H-bonds generated for 'chain 'A' and resid 16 through 19' Processing helix chain 'A' and resid 29 through 38 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'B' and resid 10 through 23 Proline residue: B 17 - end of helix Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.860A pdb=" N LYS B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 62 through 73 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.565A pdb=" N LYS B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 Processing helix chain 'B' and resid 129 through 142 Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 245 through 258 Processing helix chain 'B' and resid 263 through 279 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.638A pdb=" N LYS B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.903A pdb=" N VAL B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 432 through 454 removed outlier: 4.297A pdb=" N GLU B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 485 through 501 removed outlier: 3.618A pdb=" N HIS B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 519 Processing helix chain 'B' and resid 523 through 532 removed outlier: 4.106A pdb=" N ASP B 527 " --> pdb=" O GLU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.283A pdb=" N ASP B 540 " --> pdb=" O HIS B 536 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR B 541 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 removed outlier: 3.893A pdb=" N TYR B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER B 552 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 553 " --> pdb=" O TYR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 587 removed outlier: 4.760A pdb=" N SER B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 Proline residue: B 594 - end of helix Processing helix chain 'B' and resid 607 through 623 Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 649 through 651 No H-bonds generated for 'chain 'B' and resid 649 through 651' Processing helix chain 'B' and resid 673 through 703 removed outlier: 4.094A pdb=" N LEU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Proline residue: B 701 - end of helix Processing helix chain 'B' and resid 723 through 747 removed outlier: 3.659A pdb=" N LYS B 747 " --> pdb=" O ARG B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 767 Processing helix chain 'B' and resid 769 through 789 Processing helix chain 'B' and resid 795 through 819 removed outlier: 3.546A pdb=" N CYS B 819 " --> pdb=" O VAL B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 869 Proline residue: B 864 - end of helix Processing helix chain 'B' and resid 886 through 916 Processing helix chain 'B' and resid 932 through 970 removed outlier: 3.758A pdb=" N GLU B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR B 967 " --> pdb=" O ARG B 963 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS B 968 " --> pdb=" O LEU B 964 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS B 969 " --> pdb=" O GLU B 965 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 970 " --> pdb=" O THR B 966 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.305A pdb=" N GLY A 55 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS A 60 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL A 74 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU A 62 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLY A 72 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 108 through 113 removed outlier: 5.912A pdb=" N ARG A 153 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 130 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 825 through 827 517 hydrogen bonds defined for protein. 1500 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: 2.92 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1483 1.31 - 1.44: 2353 1.44 - 1.57: 5135 1.57 - 1.70: 1 1.70 - 1.82: 79 Bond restraints: 9051 Sorted by residual: bond pdb=" O3A CMC C 201 " pdb=" P2A CMC C 201 " ideal model delta sigma weight residual 1.674 1.510 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" C2 CMC C 201 " pdb=" O21 CMC C 201 " ideal model delta sigma weight residual 1.263 1.400 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" O6A CMC C 201 " pdb=" P2A CMC C 201 " ideal model delta sigma weight residual 1.717 1.639 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5P CMC C 201 " pdb=" C6P CMC C 201 " ideal model delta sigma weight residual 1.603 1.542 0.061 2.00e-02 2.50e+03 9.24e+00 bond pdb=" C7P CMC C 201 " pdb=" N8P CMC C 201 " ideal model delta sigma weight residual 1.521 1.469 0.052 2.00e-02 2.50e+03 6.73e+00 ... (remaining 9046 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.03: 177 106.03 - 113.02: 4865 113.02 - 120.00: 3167 120.00 - 126.99: 3917 126.99 - 133.98: 88 Bond angle restraints: 12214 Sorted by residual: angle pdb=" C1 CMC C 201 " pdb=" C2 CMC C 201 " pdb=" O21 CMC C 201 " ideal model delta sigma weight residual 119.98 108.38 11.60 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CB MET B 121 " pdb=" CG MET B 121 " pdb=" SD MET B 121 " ideal model delta sigma weight residual 112.70 124.14 -11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA GLN A 125 " pdb=" CB GLN A 125 " pdb=" CG GLN A 125 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB MET A 152 " pdb=" CG MET A 152 " pdb=" SD MET A 152 " ideal model delta sigma weight residual 112.70 121.91 -9.21 3.00e+00 1.11e-01 9.42e+00 angle pdb=" N GLY B 346 " pdb=" CA GLY B 346 " pdb=" C GLY B 346 " ideal model delta sigma weight residual 111.85 114.78 -2.93 1.06e+00 8.90e-01 7.63e+00 ... (remaining 12209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4716 17.89 - 35.79: 592 35.79 - 53.68: 158 53.68 - 71.57: 28 71.57 - 89.46: 11 Dihedral angle restraints: 5505 sinusoidal: 2297 harmonic: 3208 Sorted by residual: dihedral pdb=" CA GLU B 128 " pdb=" C GLU B 128 " pdb=" N TYR B 129 " pdb=" CA TYR B 129 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " pdb=" CD GLU B 197 " pdb=" OE1 GLU B 197 " ideal model delta sinusoidal sigma weight residual 0.00 89.46 -89.46 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP B 43 " pdb=" CB ASP B 43 " pdb=" CG ASP B 43 " pdb=" OD1 ASP B 43 " ideal model delta sinusoidal sigma weight residual -30.00 -85.86 55.86 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 961 0.029 - 0.057: 245 0.057 - 0.086: 97 0.086 - 0.115: 43 0.115 - 0.143: 4 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CB ILE B 582 " pdb=" CA ILE B 582 " pdb=" CG1 ILE B 582 " pdb=" CG2 ILE B 582 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA PRO B 323 " pdb=" N PRO B 323 " pdb=" C PRO B 323 " pdb=" CB PRO B 323 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE B 647 " pdb=" N ILE B 647 " pdb=" C ILE B 647 " pdb=" CB ILE B 647 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 1347 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 21 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 22 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 16 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO B 17 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 757 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO B 758 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 758 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 758 " -0.015 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2497 2.81 - 3.33: 9001 3.33 - 3.86: 14543 3.86 - 4.38: 15479 4.38 - 4.90: 26929 Nonbonded interactions: 68449 Sorted by model distance: nonbonded pdb=" O ASN B 167 " pdb=" OG1 THR B 171 " model vdw 2.289 2.440 nonbonded pdb=" O TYR B 149 " pdb=" OG SER B 152 " model vdw 2.314 2.440 nonbonded pdb=" OE1 GLN B 555 " pdb=" OG SER B 952 " model vdw 2.320 2.440 nonbonded pdb=" OD2 ASP B 484 " pdb=" OG1 THR B 486 " model vdw 2.353 2.440 nonbonded pdb=" N GLN B 61 " pdb=" OE1 GLN B 61 " model vdw 2.358 2.520 ... (remaining 68444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.010 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: 5.900 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 28.920 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.164 9051 Z= 0.234 Angle : 0.485 11.598 12214 Z= 0.239 Chirality : 0.034 0.143 1350 Planarity : 0.003 0.029 1555 Dihedral : 16.945 89.463 3427 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.10 % Allowed : 23.49 % Favored : 76.41 % 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: 3.32 (0.27), residues: 1074 helix: 3.43 (0.19), residues: 750 sheet: 0.10 (1.45), residues: 16 loop : -1.04 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.010 0.001 PHE B 150 TYR 0.015 0.001 TYR B 580 ARG 0.002 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.178 Fit side-chains REVERT: B 172 MET cc_start: 0.9113 (mmp) cc_final: 0.8710 (mmp) REVERT: B 340 ASN cc_start: 0.9251 (m-40) cc_final: 0.8864 (p0) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.1806 time to fit residues: 11.9498 Evaluate side-chains 40 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.0471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9051 Z= 0.231 Angle : 0.448 5.684 12214 Z= 0.227 Chirality : 0.035 0.206 1350 Planarity : 0.003 0.028 1555 Dihedral : 4.847 57.969 1203 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.54 % Allowed : 22.87 % Favored : 75.59 % 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: 3.30 (0.27), residues: 1074 helix: 3.44 (0.19), residues: 750 sheet: -0.72 (1.33), residues: 16 loop : -1.05 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 281 HIS 0.002 0.001 HIS B 834 PHE 0.026 0.001 PHE C 4 TYR 0.016 0.001 TYR B 580 ARG 0.002 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 1.136 Fit side-chains REVERT: A 148 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: B 340 ASN cc_start: 0.9313 (m-40) cc_final: 0.8959 (p0) REVERT: C 5 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.9167 (mmm) outliers start: 15 outliers final: 4 residues processed: 52 average time/residue: 0.1897 time to fit residues: 15.4222 Evaluate side-chains 42 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain C residue 5 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9051 Z= 0.187 Angle : 0.430 9.116 12214 Z= 0.216 Chirality : 0.034 0.131 1350 Planarity : 0.003 0.029 1555 Dihedral : 4.342 58.981 1203 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.95 % Allowed : 22.87 % Favored : 75.18 % 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: 3.34 (0.27), residues: 1074 helix: 3.48 (0.19), residues: 744 sheet: -1.45 (0.85), residues: 30 loop : -0.86 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.011 0.001 PHE B 150 TYR 0.016 0.001 TYR B 580 ARG 0.005 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 38 time to evaluate : 1.173 Fit side-chains REVERT: B 132 MET cc_start: 0.9267 (ptp) cc_final: 0.8989 (ptp) REVERT: B 340 ASN cc_start: 0.9319 (m-40) cc_final: 0.8994 (p0) outliers start: 19 outliers final: 10 residues processed: 53 average time/residue: 0.1604 time to fit residues: 14.1073 Evaluate side-chains 48 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain C residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 27 optimal weight: 0.0030 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.0558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9051 Z= 0.156 Angle : 0.410 6.612 12214 Z= 0.206 Chirality : 0.034 0.125 1350 Planarity : 0.003 0.030 1555 Dihedral : 4.291 59.976 1200 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.74 % Allowed : 23.59 % Favored : 74.67 % 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: 3.40 (0.27), residues: 1074 helix: 3.47 (0.19), residues: 744 sheet: -0.21 (1.16), residues: 24 loop : -0.84 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.010 0.001 PHE B 150 TYR 0.015 0.001 TYR B 580 ARG 0.002 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 39 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 148 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: B 340 ASN cc_start: 0.9329 (m-40) cc_final: 0.9023 (p0) outliers start: 17 outliers final: 10 residues processed: 52 average time/residue: 0.1942 time to fit residues: 15.5585 Evaluate side-chains 50 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain C residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 0.0000 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9051 Z= 0.152 Angle : 0.422 8.251 12214 Z= 0.210 Chirality : 0.034 0.124 1350 Planarity : 0.003 0.030 1555 Dihedral : 4.269 59.859 1200 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.56 % Allowed : 22.87 % Favored : 74.56 % 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: 3.43 (0.27), residues: 1074 helix: 3.49 (0.19), residues: 744 sheet: -0.19 (1.16), residues: 24 loop : -0.81 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.010 0.001 PHE B 150 TYR 0.015 0.001 TYR B 580 ARG 0.003 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 41 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 148 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: B 340 ASN cc_start: 0.9331 (m-40) cc_final: 0.9040 (p0) outliers start: 25 outliers final: 14 residues processed: 62 average time/residue: 0.1916 time to fit residues: 18.2583 Evaluate side-chains 55 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain C residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9051 Z= 0.247 Angle : 0.483 8.996 12214 Z= 0.238 Chirality : 0.035 0.126 1350 Planarity : 0.003 0.029 1555 Dihedral : 4.299 58.010 1200 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.85 % Allowed : 23.28 % Favored : 74.87 % 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: 3.43 (0.27), residues: 1074 helix: 3.53 (0.19), residues: 738 sheet: -0.61 (1.34), residues: 16 loop : -0.79 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 853 HIS 0.003 0.001 HIS B 116 PHE 0.010 0.001 PHE A 15 TYR 0.015 0.001 TYR B 580 ARG 0.003 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 1.220 Fit side-chains REVERT: A 148 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: A 151 ASP cc_start: 0.8819 (t0) cc_final: 0.8542 (t0) REVERT: B 121 MET cc_start: 0.9434 (mmm) cc_final: 0.9233 (mmm) REVERT: B 340 ASN cc_start: 0.9367 (m-40) cc_final: 0.9094 (p0) outliers start: 18 outliers final: 15 residues processed: 55 average time/residue: 0.1840 time to fit residues: 16.0000 Evaluate side-chains 57 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain C residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9051 Z= 0.148 Angle : 0.440 8.238 12214 Z= 0.217 Chirality : 0.034 0.124 1350 Planarity : 0.003 0.031 1555 Dihedral : 4.280 59.904 1200 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.15 % Allowed : 23.28 % Favored : 74.56 % 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: 3.48 (0.27), residues: 1074 helix: 3.52 (0.19), residues: 739 sheet: -0.41 (1.12), residues: 24 loop : -0.68 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.010 0.001 PHE B 150 TYR 0.015 0.001 TYR B 580 ARG 0.002 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 42 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 148 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: A 151 ASP cc_start: 0.8793 (t0) cc_final: 0.8515 (t0) REVERT: B 121 MET cc_start: 0.9382 (mmm) cc_final: 0.9178 (mmm) REVERT: B 340 ASN cc_start: 0.9358 (m-40) cc_final: 0.9097 (p0) REVERT: B 641 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8511 (ttm-80) outliers start: 21 outliers final: 14 residues processed: 59 average time/residue: 0.2150 time to fit residues: 19.7643 Evaluate side-chains 57 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain C residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9051 Z= 0.130 Angle : 0.436 8.385 12214 Z= 0.212 Chirality : 0.034 0.123 1350 Planarity : 0.003 0.032 1555 Dihedral : 4.226 59.647 1200 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.74 % Allowed : 23.49 % Favored : 74.77 % 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: 3.40 (0.27), residues: 1074 helix: 3.47 (0.19), residues: 745 sheet: -1.03 (0.76), residues: 46 loop : -0.73 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.026 0.001 PHE C 4 TYR 0.015 0.001 TYR B 580 ARG 0.001 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 1.102 Fit side-chains REVERT: A 148 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: A 151 ASP cc_start: 0.8788 (t0) cc_final: 0.8525 (t0) REVERT: A 152 MET cc_start: 0.8810 (mmm) cc_final: 0.8573 (mmm) REVERT: B 132 MET cc_start: 0.9523 (ptm) cc_final: 0.9166 (ptp) REVERT: B 340 ASN cc_start: 0.9354 (m-40) cc_final: 0.9107 (p0) REVERT: B 624 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: B 641 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8474 (ttm-80) outliers start: 17 outliers final: 10 residues processed: 55 average time/residue: 0.1841 time to fit residues: 15.9603 Evaluate side-chains 53 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 828 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9051 Z= 0.139 Angle : 0.467 11.440 12214 Z= 0.223 Chirality : 0.035 0.361 1350 Planarity : 0.003 0.032 1555 Dihedral : 4.240 59.931 1200 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.74 % Allowed : 23.38 % Favored : 74.87 % 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: 3.36 (0.27), residues: 1074 helix: 3.42 (0.19), residues: 745 sheet: -0.99 (0.76), residues: 46 loop : -0.68 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.009 0.001 PHE B 150 TYR 0.017 0.001 TYR B 580 ARG 0.001 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 1.067 Fit side-chains REVERT: A 148 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: A 151 ASP cc_start: 0.8770 (t0) cc_final: 0.8536 (t0) REVERT: A 152 MET cc_start: 0.8751 (mmm) cc_final: 0.8542 (mmm) REVERT: B 132 MET cc_start: 0.9529 (ptm) cc_final: 0.9163 (ptp) REVERT: B 340 ASN cc_start: 0.9356 (m-40) cc_final: 0.9119 (p0) REVERT: B 624 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8511 (mp0) outliers start: 17 outliers final: 12 residues processed: 57 average time/residue: 0.1781 time to fit residues: 16.0345 Evaluate side-chains 54 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 828 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9051 Z= 0.149 Angle : 0.471 9.787 12214 Z= 0.225 Chirality : 0.035 0.286 1350 Planarity : 0.003 0.032 1555 Dihedral : 4.239 59.537 1200 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.44 % Allowed : 23.59 % Favored : 74.97 % 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: 3.41 (0.27), residues: 1074 helix: 3.47 (0.19), residues: 740 sheet: -0.98 (0.76), residues: 46 loop : -0.62 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.023 0.001 PHE C 4 TYR 0.015 0.001 TYR B 580 ARG 0.003 0.000 ARG B 641 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 1.115 Fit side-chains REVERT: A 148 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: A 151 ASP cc_start: 0.8763 (t0) cc_final: 0.8512 (t0) REVERT: B 132 MET cc_start: 0.9528 (ptm) cc_final: 0.9171 (ptp) REVERT: B 340 ASN cc_start: 0.9355 (m-40) cc_final: 0.9125 (p0) REVERT: B 624 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8538 (mp0) outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.1609 time to fit residues: 14.0977 Evaluate side-chains 54 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 828 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.035346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.025790 restraints weight = 54982.091| |-----------------------------------------------------------------------------| r_work (start): 0.2465 rms_B_bonded: 4.64 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9051 Z= 0.125 Angle : 0.472 11.825 12214 Z= 0.223 Chirality : 0.034 0.260 1350 Planarity : 0.003 0.032 1555 Dihedral : 4.223 59.762 1200 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.23 % Allowed : 24.00 % Favored : 74.77 % 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: 3.35 (0.27), residues: 1074 helix: 3.41 (0.19), residues: 745 sheet: -0.96 (0.75), residues: 46 loop : -0.68 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 PHE 0.008 0.001 PHE B 150 TYR 0.016 0.001 TYR B 580 ARG 0.004 0.000 ARG B 641 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1607.86 seconds wall clock time: 30 minutes 19.76 seconds (1819.76 seconds total)