Starting phenix.real_space_refine on Mon Mar 11 03:26:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/03_2024/8iws_35778_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/03_2024/8iws_35778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/03_2024/8iws_35778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/03_2024/8iws_35778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/03_2024/8iws_35778_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iws_35778/03_2024/8iws_35778_updated.pdb" } resolution = 3.42 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= 0.022 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 Mg 1 5.21 5 S 52 5.16 5 Be 1 3.05 5 C 4336 2.51 5 N 1137 2.21 5 O 1278 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6809 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6803 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 854} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' CA': 1, ' MG': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.16, per 1000 atoms: 0.61 Number of scatterers: 6809 At special positions: 0 Unit cell: (93.24, 90.72, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 S 52 16.00 Mg 1 11.99 F 3 9.00 O 1278 8.00 N 1137 7.00 C 4336 6.00 Be 1 4.00 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 7 sheets defined 47.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.878A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 97 removed outlier: 3.654A pdb=" N MET A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 127 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 240 through 247 removed outlier: 3.614A pdb=" N VAL A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 287 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 310 through 328 Processing helix chain 'A' and resid 336 through 339 removed outlier: 3.605A pdb=" N GLU A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 442 through 445 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 550 through 561 removed outlier: 4.975A pdb=" N GLU A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 604 through 611 removed outlier: 5.507A pdb=" N GLN A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 610 " --> pdb=" O GLN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 646 through 653 removed outlier: 4.372A pdb=" N VAL A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.969A pdb=" N GLU A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 722 Processing helix chain 'A' and resid 731 through 741 Processing helix chain 'A' and resid 744 through 751 removed outlier: 3.986A pdb=" N GLY A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 797 Processing helix chain 'A' and resid 805 through 825 Processing helix chain 'A' and resid 843 through 859 Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 875 through 884 Processing helix chain 'A' and resid 887 through 904 Processing sheet with id= A, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.754A pdb=" N LYS A 227 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 177 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 385 through 388 removed outlier: 4.982A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 545 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 498 through 501 removed outlier: 7.712A pdb=" N LEU A 536 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR A 493 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE A 538 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER A 495 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 643 removed outlier: 3.692A pdb=" N VAL A 659 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 661 " --> pdb=" O GLY A 643 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N MET A 675 " --> pdb=" O ALA A 660 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.111A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.053A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 852 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: 2.19 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1141 1.28 - 1.41: 1484 1.41 - 1.55: 4195 1.55 - 1.68: 10 1.68 - 1.81: 84 Bond restraints: 6914 Sorted by residual: bond pdb=" C ASP A 350 " pdb=" O ASP A 350 " ideal model delta sigma weight residual 1.236 1.148 0.088 1.24e-02 6.50e+03 5.06e+01 bond pdb=" CA ASP A 350 " pdb=" CB ASP A 350 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.35e-02 5.49e+03 3.62e+01 bond pdb=" CA PRO A 762 " pdb=" CB PRO A 762 " ideal model delta sigma weight residual 1.536 1.473 0.063 1.37e-02 5.33e+03 2.09e+01 bond pdb=" C PRO A 762 " pdb=" O PRO A 762 " ideal model delta sigma weight residual 1.240 1.192 0.048 1.12e-02 7.97e+03 1.86e+01 bond pdb=" BE BEF A1003 " pdb=" F2 BEF A1003 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 6909 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.58: 181 106.58 - 113.43: 3932 113.43 - 120.28: 2286 120.28 - 127.13: 2914 127.13 - 133.99: 49 Bond angle restraints: 9362 Sorted by residual: angle pdb=" C ASP A 350 " pdb=" N LYS A 351 " pdb=" CA LYS A 351 " ideal model delta sigma weight residual 120.28 133.16 -12.88 1.34e+00 5.57e-01 9.25e+01 angle pdb=" CA ASP A 350 " pdb=" C ASP A 350 " pdb=" N LYS A 351 " ideal model delta sigma weight residual 116.39 126.88 -10.49 1.26e+00 6.30e-01 6.93e+01 angle pdb=" O SER A 349 " pdb=" C SER A 349 " pdb=" N ASP A 350 " ideal model delta sigma weight residual 123.48 114.91 8.57 1.14e+00 7.69e-01 5.65e+01 angle pdb=" C PRO A 762 " pdb=" N PRO A 763 " pdb=" CA PRO A 763 " ideal model delta sigma weight residual 119.90 126.33 -6.43 1.02e+00 9.61e-01 3.98e+01 angle pdb=" C PRO A 30 " pdb=" CA PRO A 30 " pdb=" CB PRO A 30 " ideal model delta sigma weight residual 111.56 101.37 10.19 1.65e+00 3.67e-01 3.81e+01 ... (remaining 9357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3603 17.84 - 35.68: 484 35.68 - 53.52: 115 53.52 - 71.36: 16 71.36 - 89.19: 8 Dihedral angle restraints: 4226 sinusoidal: 1664 harmonic: 2562 Sorted by residual: dihedral pdb=" C PRO A 30 " pdb=" N PRO A 30 " pdb=" CA PRO A 30 " pdb=" CB PRO A 30 " ideal model delta harmonic sigma weight residual -120.70 -108.53 -12.17 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" N ASP A 350 " pdb=" C ASP A 350 " pdb=" CA ASP A 350 " pdb=" CB ASP A 350 " ideal model delta harmonic sigma weight residual 122.80 110.99 11.81 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" C ASP A 350 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " pdb=" CB ASP A 350 " ideal model delta harmonic sigma weight residual -122.60 -112.43 -10.17 0 2.50e+00 1.60e-01 1.66e+01 ... (remaining 4223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 805 0.036 - 0.073: 240 0.073 - 0.109: 67 0.109 - 0.146: 15 0.146 - 0.182: 1 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA ILE A 545 " pdb=" N ILE A 545 " pdb=" C ILE A 545 " pdb=" CB ILE A 545 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ASP A 350 " pdb=" N ASP A 350 " pdb=" C ASP A 350 " pdb=" CB ASP A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1125 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 349 " 0.019 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C SER A 349 " -0.062 2.00e-02 2.50e+03 pdb=" O SER A 349 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP A 350 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 29 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C LEU A 29 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A 29 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO A 30 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 452 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO A 453 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.029 5.00e-02 4.00e+02 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 10 2.39 - 3.01: 3824 3.01 - 3.64: 10255 3.64 - 4.27: 14359 4.27 - 4.90: 24768 Nonbonded interactions: 53216 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" F1 BEF A1003 " model vdw 1.757 2.120 nonbonded pdb=" OD1 ASP A 644 " pdb="MG MG A1001 " model vdw 1.804 2.170 nonbonded pdb=" O THR A 352 " pdb="MG MG A1001 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASP A 350 " pdb=" BE BEF A1003 " model vdw 2.098 1.936 nonbonded pdb=" O ARG A 417 " pdb=" OG1 THR A 420 " model vdw 2.252 2.440 ... (remaining 53211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.110 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.970 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 0.088 6914 Z= 0.229 Angle : 0.655 13.764 9362 Z= 0.380 Chirality : 0.039 0.182 1128 Planarity : 0.004 0.053 1183 Dihedral : 16.815 89.194 2568 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.92 % Allowed : 25.26 % Favored : 73.82 % Cbeta Deviations : 0.24 % 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: 2.06 (0.30), residues: 888 helix: 2.83 (0.25), residues: 431 sheet: 0.63 (0.55), residues: 99 loop : -0.25 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 766 HIS 0.001 0.000 HIS A 58 PHE 0.008 0.001 PHE A 454 TYR 0.004 0.000 TYR A 587 ARG 0.007 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 629 ILE cc_start: 0.7533 (mm) cc_final: 0.7227 (mm) outliers start: 7 outliers final: 4 residues processed: 108 average time/residue: 0.1893 time to fit residues: 27.3505 Evaluate side-chains 104 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 843 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 0.0040 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A 865 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6914 Z= 0.186 Angle : 0.526 8.771 9362 Z= 0.277 Chirality : 0.040 0.146 1128 Planarity : 0.005 0.049 1183 Dihedral : 3.975 35.279 946 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.06 % Allowed : 24.48 % Favored : 71.47 % 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: 1.48 (0.30), residues: 888 helix: 2.11 (0.24), residues: 439 sheet: 0.16 (0.53), residues: 99 loop : -0.17 (0.38), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 460 HIS 0.003 0.001 HIS A 467 PHE 0.020 0.001 PHE A 118 TYR 0.012 0.001 TYR A 618 ARG 0.005 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7503 (mmm) cc_final: 0.6709 (mtt) REVERT: A 686 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6146 (tpt) outliers start: 31 outliers final: 19 residues processed: 137 average time/residue: 0.1767 time to fit residues: 33.2132 Evaluate side-chains 133 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6914 Z= 0.234 Angle : 0.568 9.273 9362 Z= 0.298 Chirality : 0.042 0.142 1128 Planarity : 0.005 0.045 1183 Dihedral : 4.129 19.339 938 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.10 % Allowed : 25.92 % Favored : 68.98 % 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: 0.79 (0.29), residues: 888 helix: 1.43 (0.24), residues: 445 sheet: 0.18 (0.51), residues: 110 loop : -0.53 (0.38), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 766 HIS 0.002 0.001 HIS A 149 PHE 0.014 0.001 PHE A 176 TYR 0.019 0.001 TYR A 618 ARG 0.008 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7810 (mmm) cc_final: 0.7422 (mtt) REVERT: A 276 ILE cc_start: 0.8682 (tp) cc_final: 0.8234 (mt) REVERT: A 287 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8412 (mm) REVERT: A 767 LYS cc_start: 0.7846 (pttm) cc_final: 0.7639 (pttm) REVERT: A 784 ILE cc_start: 0.8430 (mt) cc_final: 0.8222 (mt) outliers start: 39 outliers final: 23 residues processed: 161 average time/residue: 0.1795 time to fit residues: 39.0823 Evaluate side-chains 147 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6914 Z= 0.194 Angle : 0.534 6.563 9362 Z= 0.279 Chirality : 0.041 0.153 1128 Planarity : 0.005 0.048 1183 Dihedral : 3.986 20.008 938 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.45 % Allowed : 28.14 % Favored : 67.41 % 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: 0.76 (0.30), residues: 888 helix: 1.45 (0.25), residues: 445 sheet: 0.17 (0.48), residues: 125 loop : -0.64 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 766 HIS 0.002 0.000 HIS A 467 PHE 0.012 0.001 PHE A 176 TYR 0.017 0.001 TYR A 618 ARG 0.005 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7792 (mmm) cc_final: 0.7470 (mtt) REVERT: A 287 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8419 (mm) REVERT: A 657 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8268 (tp) outliers start: 34 outliers final: 20 residues processed: 150 average time/residue: 0.1688 time to fit residues: 34.5928 Evaluate side-chains 144 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 418 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6914 Z= 0.179 Angle : 0.527 7.279 9362 Z= 0.274 Chirality : 0.040 0.160 1128 Planarity : 0.005 0.050 1183 Dihedral : 3.942 18.049 938 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.84 % Allowed : 27.62 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.30), residues: 888 helix: 1.46 (0.25), residues: 445 sheet: 0.17 (0.51), residues: 115 loop : -0.67 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 766 HIS 0.001 0.000 HIS A 149 PHE 0.011 0.001 PHE A 176 TYR 0.015 0.001 TYR A 618 ARG 0.005 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 0.822 Fit side-chains REVERT: A 97 MET cc_start: 0.7732 (mmm) cc_final: 0.7525 (mtt) REVERT: A 287 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8415 (mm) REVERT: A 449 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8097 (mptt) outliers start: 37 outliers final: 26 residues processed: 147 average time/residue: 0.1776 time to fit residues: 36.1559 Evaluate side-chains 148 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.0270 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN A 727 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6914 Z= 0.186 Angle : 0.529 7.752 9362 Z= 0.274 Chirality : 0.040 0.164 1128 Planarity : 0.005 0.050 1183 Dihedral : 3.928 17.453 938 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.84 % Allowed : 28.01 % Favored : 67.15 % 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: 0.68 (0.29), residues: 888 helix: 1.49 (0.25), residues: 443 sheet: -0.31 (0.54), residues: 93 loop : -0.63 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 766 HIS 0.001 0.000 HIS A 467 PHE 0.011 0.001 PHE A 176 TYR 0.015 0.001 TYR A 618 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 0.696 Fit side-chains REVERT: A 248 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7649 (ttt) REVERT: A 276 ILE cc_start: 0.8679 (tp) cc_final: 0.8250 (mt) REVERT: A 287 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8415 (mm) outliers start: 37 outliers final: 25 residues processed: 152 average time/residue: 0.1581 time to fit residues: 33.4339 Evaluate side-chains 156 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 853 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6914 Z= 0.297 Angle : 0.625 8.395 9362 Z= 0.321 Chirality : 0.043 0.239 1128 Planarity : 0.005 0.053 1183 Dihedral : 4.536 22.941 938 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.37 % Allowed : 28.14 % Favored : 66.49 % 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: 0.26 (0.29), residues: 888 helix: 1.11 (0.25), residues: 445 sheet: -0.07 (0.56), residues: 87 loop : -0.92 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 795 HIS 0.003 0.001 HIS A 364 PHE 0.017 0.001 PHE A 176 TYR 0.018 0.001 TYR A 618 ARG 0.008 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 0.802 Fit side-chains REVERT: A 87 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8149 (mp) REVERT: A 248 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7880 (ttt) REVERT: A 287 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 810 MET cc_start: 0.7947 (mmm) cc_final: 0.7712 (mmm) outliers start: 41 outliers final: 25 residues processed: 165 average time/residue: 0.1724 time to fit residues: 38.7531 Evaluate side-chains 163 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 861 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6914 Z= 0.216 Angle : 0.590 8.486 9362 Z= 0.304 Chirality : 0.041 0.189 1128 Planarity : 0.005 0.053 1183 Dihedral : 4.293 17.967 938 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.58 % Allowed : 29.32 % Favored : 66.10 % 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: 0.28 (0.29), residues: 888 helix: 1.14 (0.25), residues: 447 sheet: -0.09 (0.54), residues: 97 loop : -0.95 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 766 HIS 0.002 0.000 HIS A 467 PHE 0.013 0.001 PHE A 725 TYR 0.015 0.001 TYR A 618 ARG 0.005 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 0.672 Fit side-chains REVERT: A 248 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7816 (ttt) REVERT: A 287 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8411 (mm) REVERT: A 810 MET cc_start: 0.7751 (mmm) cc_final: 0.7467 (mmm) outliers start: 35 outliers final: 29 residues processed: 156 average time/residue: 0.1666 time to fit residues: 36.2116 Evaluate side-chains 161 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 861 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6914 Z= 0.238 Angle : 0.598 8.782 9362 Z= 0.307 Chirality : 0.042 0.240 1128 Planarity : 0.005 0.054 1183 Dihedral : 4.318 18.793 938 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.19 % Allowed : 29.45 % Favored : 66.36 % 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: 0.20 (0.29), residues: 888 helix: 1.07 (0.25), residues: 456 sheet: -0.34 (0.57), residues: 87 loop : -0.94 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 766 HIS 0.002 0.001 HIS A 364 PHE 0.014 0.001 PHE A 176 TYR 0.017 0.001 TYR A 618 ARG 0.002 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 0.767 Fit side-chains REVERT: A 248 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7878 (ttt) REVERT: A 287 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8414 (mm) REVERT: A 810 MET cc_start: 0.7796 (mmm) cc_final: 0.7525 (mmm) outliers start: 32 outliers final: 26 residues processed: 151 average time/residue: 0.1698 time to fit residues: 35.0979 Evaluate side-chains 157 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 861 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.0000 chunk 70 optimal weight: 0.0050 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6914 Z= 0.191 Angle : 0.580 9.688 9362 Z= 0.296 Chirality : 0.041 0.203 1128 Planarity : 0.005 0.053 1183 Dihedral : 4.103 18.558 938 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.53 % Allowed : 29.97 % Favored : 66.49 % 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: 0.42 (0.30), residues: 888 helix: 1.30 (0.25), residues: 453 sheet: -0.26 (0.55), residues: 97 loop : -0.90 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 766 HIS 0.002 0.000 HIS A 58 PHE 0.010 0.001 PHE A 725 TYR 0.012 0.001 TYR A 618 ARG 0.003 0.000 ARG A 900 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.581 Fit side-chains REVERT: A 287 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8377 (mm) REVERT: A 602 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.3693 (ptt) REVERT: A 810 MET cc_start: 0.7682 (mmm) cc_final: 0.7458 (mmm) outliers start: 27 outliers final: 20 residues processed: 146 average time/residue: 0.1654 time to fit residues: 33.9447 Evaluate side-chains 150 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 861 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 0.0170 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.183938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156197 restraints weight = 8356.646| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.83 r_work: 0.3655 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6914 Z= 0.196 Angle : 0.591 12.537 9362 Z= 0.299 Chirality : 0.041 0.208 1128 Planarity : 0.005 0.054 1183 Dihedral : 4.086 18.549 938 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.40 % Allowed : 29.84 % Favored : 66.75 % 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: 0.46 (0.30), residues: 888 helix: 1.30 (0.25), residues: 454 sheet: -0.27 (0.55), residues: 97 loop : -0.84 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 766 HIS 0.002 0.001 HIS A 467 PHE 0.011 0.001 PHE A 176 TYR 0.015 0.001 TYR A 618 ARG 0.003 0.000 ARG A 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.87 seconds wall clock time: 37 minutes 19.04 seconds (2239.04 seconds total)