Starting phenix.real_space_refine on Tue Sep 24 00:41:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/09_2024/7rav_24387.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/09_2024/7rav_24387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/09_2024/7rav_24387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/09_2024/7rav_24387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/09_2024/7rav_24387.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/09_2024/7rav_24387.cif" } resolution = 3.3 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 40 atoms to isotropic. 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 3 5.49 5 S 39 5.16 5 C 3976 2.51 5 N 1046 2.21 5 O 1151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6215 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6184 Classifications: {'peptide': 773} Link IDs: {'PTRANS': 26, 'TRANS': 746} Chain breaks: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.14, per 1000 atoms: 0.67 Number of scatterers: 6215 At special positions: 0 Unit cell: (74.858, 78.0662, 133.675, 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 39 16.00 P 3 15.00 O 1151 8.00 N 1046 7.00 C 3976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 902.5 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1460 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 46.6% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 64 through 70 removed outlier: 4.092A pdb=" N THR A 69 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.511A pdb=" N ALA A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.782A pdb=" N GLN A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.022A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.668A pdb=" N ARG A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.639A pdb=" N THR A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 418 Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.711A pdb=" N PHE A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 492 through 498 removed outlier: 3.668A pdb=" N LEU A 495 " --> pdb=" O CYS A 492 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 531 through 542 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.541A pdb=" N THR A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.506A pdb=" N ILE A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 651 Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.764A pdb=" N THR A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 704 removed outlier: 4.203A pdb=" N LEU A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 703 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 717 removed outlier: 3.809A pdb=" N LEU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.636A pdb=" N THR A 726 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 763 Processing helix chain 'A' and resid 765 through 778 removed outlier: 4.432A pdb=" N LEU A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY A 772 " --> pdb=" O ASP A 768 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 788 removed outlier: 3.607A pdb=" N SER A 788 " --> pdb=" O LYS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.945A pdb=" N VAL A 796 " --> pdb=" O PHE A 792 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 792 through 797' Processing helix chain 'A' and resid 803 through 814 removed outlier: 4.569A pdb=" N THR A 807 " --> pdb=" O LYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 878 removed outlier: 3.993A pdb=" N THR A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.553A pdb=" N LEU A 914 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 468 removed outlier: 6.714A pdb=" N MET A 466 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL A 546 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 578 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE A 548 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA A 580 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU A 550 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 500 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A 549 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 502 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP A 551 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 504 " --> pdb=" O ASP A 551 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 199 hydrogen bonds defined for protein. 555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1961 1.34 - 1.46: 1377 1.46 - 1.58: 2962 1.58 - 1.70: 5 1.70 - 1.83: 52 Bond restraints: 6357 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.24e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C8 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.11e+01 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.01e+01 bond pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.00e-02 1.00e+04 1.89e+01 ... (remaining 6352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 8527 4.13 - 8.25: 60 8.25 - 12.38: 4 12.38 - 16.50: 0 16.50 - 20.63: 2 Bond angle restraints: 8593 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 119.24 20.63 1.00e+00 1.00e+00 4.26e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 118.98 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" N GLY A 175 " pdb=" CA GLY A 175 " pdb=" C GLY A 175 " ideal model delta sigma weight residual 112.73 100.90 11.83 1.20e+00 6.94e-01 9.72e+01 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.62e+01 angle pdb=" N3 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 127.04 134.79 -7.75 1.15e+00 7.59e-01 4.56e+01 ... (remaining 8588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3348 17.97 - 35.93: 371 35.93 - 53.90: 71 53.90 - 71.86: 15 71.86 - 89.83: 11 Dihedral angle restraints: 3816 sinusoidal: 1559 harmonic: 2257 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 124 " pdb=" CB CYS A 124 " ideal model delta sinusoidal sigma weight residual 93.00 48.56 44.44 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA HIS A 157 " pdb=" C HIS A 157 " pdb=" N GLU A 158 " pdb=" CA GLU A 158 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE A 135 " pdb=" C ILE A 135 " pdb=" N GLY A 136 " pdb=" CA GLY A 136 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 3813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 756 0.058 - 0.117: 170 0.117 - 0.175: 18 0.175 - 0.233: 2 0.233 - 0.292: 1 Chirality restraints: 947 Sorted by residual: chirality pdb=" CA PRO A 340 " pdb=" N PRO A 340 " pdb=" C PRO A 340 " pdb=" CB PRO A 340 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA HIS A 174 " pdb=" N HIS A 174 " pdb=" C HIS A 174 " pdb=" CB HIS A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA GLN A 766 " pdb=" N GLN A 766 " pdb=" C GLN A 766 " pdb=" CB GLN A 766 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 944 not shown) Planarity restraints: 1089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 339 " 0.061 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO A 340 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 492 " -0.038 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 493 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 330 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO A 331 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.032 5.00e-02 4.00e+02 ... (remaining 1086 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1067 2.76 - 3.29: 6528 3.29 - 3.83: 9907 3.83 - 4.36: 11611 4.36 - 4.90: 18876 Nonbonded interactions: 47989 Sorted by model distance: nonbonded pdb=" OH TYR A 172 " pdb=" NH2 ARG A 261 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS A 723 " pdb=" OG1 THR A 725 " model vdw 2.224 3.120 nonbonded pdb=" NH1 ARG A 314 " pdb=" O THR A 430 " model vdw 2.242 3.120 nonbonded pdb=" OG SER A 554 " pdb=" OG SER A 558 " model vdw 2.247 3.040 nonbonded pdb=" O ASN A 900 " pdb=" ND2 ASN A 900 " model vdw 2.248 3.120 ... (remaining 47984 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=0.00 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 17.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6357 Z= 0.282 Angle : 0.930 20.628 8593 Z= 0.590 Chirality : 0.049 0.292 947 Planarity : 0.005 0.092 1089 Dihedral : 15.924 89.826 2350 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.73 % Favored : 82.88 % Rotamer: Outliers : 1.17 % Allowed : 0.44 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.29), residues: 765 helix: -0.98 (0.29), residues: 313 sheet: -1.74 (0.75), residues: 37 loop : -3.46 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.006 0.001 HIS A 582 PHE 0.027 0.002 PHE A 859 TYR 0.037 0.002 TYR A 496 ARG 0.008 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7514 (tpp) cc_final: 0.7266 (tpp) REVERT: A 57 MET cc_start: 0.7615 (ptp) cc_final: 0.7405 (ptp) REVERT: A 148 MET cc_start: 0.6317 (tmm) cc_final: 0.6110 (tmm) REVERT: A 160 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 164 GLU cc_start: 0.7523 (pp20) cc_final: 0.7231 (pp20) REVERT: A 167 GLU cc_start: 0.7299 (mp0) cc_final: 0.6992 (mp0) REVERT: A 332 MET cc_start: 0.5342 (pmm) cc_final: 0.5045 (pmm) REVERT: A 408 ARG cc_start: 0.7768 (tmm-80) cc_final: 0.7230 (tmm-80) REVERT: A 443 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7908 (mtmm) REVERT: A 535 LEU cc_start: 0.8699 (tp) cc_final: 0.8470 (tp) REVERT: A 551 ASP cc_start: 0.7114 (t70) cc_final: 0.6681 (t0) REVERT: A 598 GLU cc_start: 0.6899 (tt0) cc_final: 0.6650 (tt0) REVERT: A 630 ILE cc_start: 0.8585 (tp) cc_final: 0.8332 (tp) REVERT: A 651 ASP cc_start: 0.7321 (t0) cc_final: 0.7087 (t0) REVERT: A 812 LEU cc_start: 0.8393 (mt) cc_final: 0.8094 (mt) REVERT: A 814 GLN cc_start: 0.7762 (pp30) cc_final: 0.7405 (pp30) REVERT: A 865 LEU cc_start: 0.8483 (mm) cc_final: 0.8281 (mm) REVERT: A 867 LEU cc_start: 0.8955 (pp) cc_final: 0.8365 (pp) REVERT: A 869 LEU cc_start: 0.8422 (mm) cc_final: 0.8213 (mm) REVERT: A 871 PHE cc_start: 0.7230 (m-80) cc_final: 0.6856 (m-80) outliers start: 8 outliers final: 0 residues processed: 228 average time/residue: 0.2115 time to fit residues: 61.0197 Evaluate side-chains 198 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6357 Z= 0.248 Angle : 0.766 9.101 8593 Z= 0.401 Chirality : 0.047 0.169 947 Planarity : 0.005 0.051 1089 Dihedral : 7.754 82.917 871 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.82 % Favored : 83.92 % Rotamer: Outliers : 1.46 % Allowed : 13.47 % Favored : 85.07 % 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: -3.07 (0.30), residues: 765 helix: -0.52 (0.30), residues: 325 sheet: -1.76 (0.76), residues: 37 loop : -3.56 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 220 HIS 0.004 0.001 HIS A 253 PHE 0.052 0.002 PHE A 792 TYR 0.045 0.003 TYR A 496 ARG 0.006 0.001 ARG A 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 216 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7521 (tpp) cc_final: 0.7219 (tpp) REVERT: A 57 MET cc_start: 0.7592 (ptp) cc_final: 0.7369 (ptp) REVERT: A 62 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7936 (mtmm) REVERT: A 138 TYR cc_start: 0.6918 (t80) cc_final: 0.6617 (t80) REVERT: A 148 MET cc_start: 0.6381 (tmm) cc_final: 0.6120 (tmm) REVERT: A 160 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 164 GLU cc_start: 0.7520 (pp20) cc_final: 0.7058 (pp20) REVERT: A 167 GLU cc_start: 0.7320 (mp0) cc_final: 0.6776 (mp0) REVERT: A 223 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8120 (mtmm) REVERT: A 332 MET cc_start: 0.5364 (pmm) cc_final: 0.4953 (pmm) REVERT: A 408 ARG cc_start: 0.7731 (tmm-80) cc_final: 0.7202 (tmm-80) REVERT: A 423 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 443 LYS cc_start: 0.8523 (mtmm) cc_final: 0.7962 (mtmm) REVERT: A 454 THR cc_start: 0.8362 (p) cc_final: 0.7987 (t) REVERT: A 455 ILE cc_start: 0.8457 (mm) cc_final: 0.7988 (tp) REVERT: A 457 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 535 LEU cc_start: 0.8736 (tp) cc_final: 0.8514 (tp) REVERT: A 551 ASP cc_start: 0.7208 (t70) cc_final: 0.6688 (t0) REVERT: A 630 ILE cc_start: 0.8662 (tp) cc_final: 0.8325 (tp) REVERT: A 766 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7601 (pp30) REVERT: A 812 LEU cc_start: 0.8452 (mt) cc_final: 0.8113 (mt) REVERT: A 814 GLN cc_start: 0.7847 (pp30) cc_final: 0.7455 (pp30) REVERT: A 863 HIS cc_start: 0.7262 (m90) cc_final: 0.6573 (m90) REVERT: A 865 LEU cc_start: 0.8511 (mm) cc_final: 0.8282 (mm) REVERT: A 867 LEU cc_start: 0.8924 (pp) cc_final: 0.8348 (pp) REVERT: A 869 LEU cc_start: 0.8491 (mm) cc_final: 0.8274 (mm) REVERT: A 871 PHE cc_start: 0.7214 (m-80) cc_final: 0.6752 (m-80) REVERT: A 873 TYR cc_start: 0.7426 (t80) cc_final: 0.7021 (t80) outliers start: 10 outliers final: 7 residues processed: 219 average time/residue: 0.2145 time to fit residues: 58.8010 Evaluate side-chains 204 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 197 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 731 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 23 optimal weight: 0.0270 chunk 56 optimal weight: 0.9980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6357 Z= 0.194 Angle : 0.708 8.892 8593 Z= 0.369 Chirality : 0.045 0.171 947 Planarity : 0.005 0.056 1089 Dihedral : 7.429 80.852 871 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.90 % Favored : 84.84 % Rotamer: Outliers : 2.34 % Allowed : 18.45 % Favored : 79.21 % 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: -2.92 (0.30), residues: 765 helix: -0.22 (0.31), residues: 317 sheet: -1.93 (0.70), residues: 37 loop : -3.55 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.006 0.001 HIS A 811 PHE 0.035 0.002 PHE A 792 TYR 0.041 0.002 TYR A 496 ARG 0.006 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 0.598 Fit side-chains REVERT: A 47 MET cc_start: 0.7555 (tpp) cc_final: 0.7258 (tpp) REVERT: A 62 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7913 (mtmm) REVERT: A 92 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6998 (mtm110) REVERT: A 148 MET cc_start: 0.6292 (tmm) cc_final: 0.6031 (tmm) REVERT: A 160 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7073 (tm-30) REVERT: A 164 GLU cc_start: 0.7509 (pp20) cc_final: 0.7212 (pp20) REVERT: A 167 GLU cc_start: 0.7284 (mp0) cc_final: 0.6876 (mp0) REVERT: A 206 ASN cc_start: 0.8070 (m-40) cc_final: 0.7698 (m110) REVERT: A 208 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6761 (mm-30) REVERT: A 223 LYS cc_start: 0.8326 (mtmm) cc_final: 0.8039 (mtmm) REVERT: A 226 PHE cc_start: 0.8685 (t80) cc_final: 0.8085 (t80) REVERT: A 332 MET cc_start: 0.5354 (pmm) cc_final: 0.4904 (pmm) REVERT: A 408 ARG cc_start: 0.7693 (tmm-80) cc_final: 0.7218 (tmm-80) REVERT: A 423 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 443 LYS cc_start: 0.8468 (mtmm) cc_final: 0.7907 (mtmm) REVERT: A 454 THR cc_start: 0.8307 (p) cc_final: 0.8068 (t) REVERT: A 455 ILE cc_start: 0.8485 (mm) cc_final: 0.8024 (tp) REVERT: A 457 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 551 ASP cc_start: 0.7179 (t70) cc_final: 0.6654 (t0) REVERT: A 570 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7299 (t0) REVERT: A 585 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.8133 (mmm-85) REVERT: A 624 LYS cc_start: 0.8013 (tptm) cc_final: 0.7652 (tttm) REVERT: A 630 ILE cc_start: 0.8617 (tp) cc_final: 0.8302 (tp) REVERT: A 723 LYS cc_start: 0.8062 (tmtt) cc_final: 0.7601 (tmtt) REVERT: A 766 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7731 (pp30) REVERT: A 812 LEU cc_start: 0.8391 (mt) cc_final: 0.8074 (mt) REVERT: A 814 GLN cc_start: 0.7923 (pp30) cc_final: 0.7507 (pp30) REVERT: A 863 HIS cc_start: 0.7327 (m90) cc_final: 0.6666 (m90) REVERT: A 865 LEU cc_start: 0.8466 (mm) cc_final: 0.8231 (mm) REVERT: A 867 LEU cc_start: 0.8894 (pp) cc_final: 0.8322 (pp) REVERT: A 871 PHE cc_start: 0.7209 (m-80) cc_final: 0.6756 (m-80) REVERT: A 873 TYR cc_start: 0.7466 (t80) cc_final: 0.7025 (t80) outliers start: 16 outliers final: 10 residues processed: 211 average time/residue: 0.2083 time to fit residues: 55.4211 Evaluate side-chains 210 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 779 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 70 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6357 Z= 0.232 Angle : 0.713 8.637 8593 Z= 0.372 Chirality : 0.046 0.186 947 Planarity : 0.005 0.055 1089 Dihedral : 7.324 77.045 871 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.16 % Favored : 84.71 % Rotamer: Outliers : 2.93 % Allowed : 21.23 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.85 (0.30), residues: 765 helix: -0.13 (0.31), residues: 317 sheet: -1.89 (0.70), residues: 37 loop : -3.54 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS A 811 PHE 0.037 0.002 PHE A 792 TYR 0.031 0.002 TYR A 496 ARG 0.005 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 0.658 Fit side-chains REVERT: A 47 MET cc_start: 0.7540 (tpp) cc_final: 0.7234 (tpp) REVERT: A 92 ARG cc_start: 0.7234 (mtm110) cc_final: 0.7024 (mtm110) REVERT: A 138 TYR cc_start: 0.6780 (t80) cc_final: 0.6565 (t80) REVERT: A 148 MET cc_start: 0.6319 (tmm) cc_final: 0.6039 (tmm) REVERT: A 160 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 206 ASN cc_start: 0.8398 (m110) cc_final: 0.8107 (m-40) REVERT: A 208 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6811 (mm-30) REVERT: A 223 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8054 (mtmm) REVERT: A 226 PHE cc_start: 0.8668 (t80) cc_final: 0.8358 (t80) REVERT: A 332 MET cc_start: 0.5353 (pmm) cc_final: 0.4944 (pmm) REVERT: A 408 ARG cc_start: 0.7716 (tmm-80) cc_final: 0.7361 (tmm-80) REVERT: A 409 ASP cc_start: 0.7583 (t0) cc_final: 0.7326 (t0) REVERT: A 443 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7854 (mtmm) REVERT: A 455 ILE cc_start: 0.8562 (mm) cc_final: 0.8062 (tp) REVERT: A 457 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 551 ASP cc_start: 0.7222 (t70) cc_final: 0.6814 (t70) REVERT: A 624 LYS cc_start: 0.8068 (tptm) cc_final: 0.7717 (tttm) REVERT: A 630 ILE cc_start: 0.8630 (tp) cc_final: 0.8335 (tp) REVERT: A 723 LYS cc_start: 0.8078 (tmtt) cc_final: 0.7645 (tmtt) REVERT: A 766 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7768 (pp30) REVERT: A 778 GLN cc_start: 0.7857 (mp10) cc_final: 0.7553 (mp10) REVERT: A 812 LEU cc_start: 0.8397 (mt) cc_final: 0.8083 (mt) REVERT: A 814 GLN cc_start: 0.7941 (pp30) cc_final: 0.7499 (pp30) REVERT: A 863 HIS cc_start: 0.7388 (m90) cc_final: 0.6725 (m90) REVERT: A 865 LEU cc_start: 0.8506 (mm) cc_final: 0.8300 (mm) REVERT: A 867 LEU cc_start: 0.8913 (pp) cc_final: 0.8371 (pp) REVERT: A 871 PHE cc_start: 0.7314 (m-80) cc_final: 0.6872 (m-80) REVERT: A 873 TYR cc_start: 0.7443 (t80) cc_final: 0.7047 (t80) outliers start: 20 outliers final: 13 residues processed: 213 average time/residue: 0.2087 time to fit residues: 56.2738 Evaluate side-chains 210 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 900 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 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 96 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 887 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6357 Z= 0.240 Angle : 0.727 8.514 8593 Z= 0.373 Chirality : 0.046 0.158 947 Planarity : 0.005 0.054 1089 Dihedral : 7.277 73.443 871 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.82 % Favored : 84.05 % Rotamer: Outliers : 3.07 % Allowed : 22.40 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.86 (0.30), residues: 765 helix: -0.24 (0.30), residues: 324 sheet: -1.99 (0.69), residues: 37 loop : -3.49 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS A 811 PHE 0.028 0.002 PHE A 792 TYR 0.026 0.002 TYR A 496 ARG 0.005 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 0.710 Fit side-chains REVERT: A 47 MET cc_start: 0.7537 (tpp) cc_final: 0.7235 (tpp) REVERT: A 119 LYS cc_start: 0.8654 (tppp) cc_final: 0.8268 (tppp) REVERT: A 148 MET cc_start: 0.6316 (tmm) cc_final: 0.6020 (tmm) REVERT: A 160 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 164 GLU cc_start: 0.7869 (pp20) cc_final: 0.7493 (pp20) REVERT: A 167 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7380 (mm-30) REVERT: A 172 TYR cc_start: 0.6911 (m-80) cc_final: 0.6701 (m-80) REVERT: A 208 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6803 (mm-30) REVERT: A 223 LYS cc_start: 0.8343 (mtmm) cc_final: 0.8037 (mtmm) REVERT: A 226 PHE cc_start: 0.8692 (t80) cc_final: 0.8346 (t80) REVERT: A 260 ARG cc_start: 0.6646 (mpp-170) cc_final: 0.6377 (mpp-170) REVERT: A 332 MET cc_start: 0.5360 (pmm) cc_final: 0.4949 (pmm) REVERT: A 408 ARG cc_start: 0.7715 (tmm-80) cc_final: 0.7404 (tmm-80) REVERT: A 409 ASP cc_start: 0.7551 (t0) cc_final: 0.7231 (t0) REVERT: A 441 ILE cc_start: 0.8182 (mp) cc_final: 0.7959 (mm) REVERT: A 443 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8116 (mtmm) REVERT: A 457 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 532 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 551 ASP cc_start: 0.7232 (t70) cc_final: 0.6842 (t70) REVERT: A 570 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7564 (t160) REVERT: A 624 LYS cc_start: 0.8075 (tptm) cc_final: 0.7702 (tttm) REVERT: A 630 ILE cc_start: 0.8629 (tp) cc_final: 0.8342 (tp) REVERT: A 712 ASP cc_start: 0.8162 (m-30) cc_final: 0.7778 (m-30) REVERT: A 723 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7664 (tmtt) REVERT: A 747 LEU cc_start: 0.8227 (mm) cc_final: 0.8001 (mm) REVERT: A 778 GLN cc_start: 0.7926 (mp10) cc_final: 0.7590 (mp10) REVERT: A 812 LEU cc_start: 0.8367 (mt) cc_final: 0.8042 (mt) REVERT: A 814 GLN cc_start: 0.7931 (pp30) cc_final: 0.7495 (pp30) REVERT: A 865 LEU cc_start: 0.8544 (mm) cc_final: 0.8217 (mt) REVERT: A 867 LEU cc_start: 0.8916 (pp) cc_final: 0.8390 (pp) REVERT: A 871 PHE cc_start: 0.7306 (m-80) cc_final: 0.6917 (m-80) REVERT: A 873 TYR cc_start: 0.7405 (t80) cc_final: 0.6963 (t80) outliers start: 21 outliers final: 15 residues processed: 214 average time/residue: 0.2139 time to fit residues: 57.5110 Evaluate side-chains 223 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 887 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6357 Z= 0.234 Angle : 0.739 10.975 8593 Z= 0.378 Chirality : 0.047 0.288 947 Planarity : 0.005 0.053 1089 Dihedral : 7.236 72.072 871 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.95 % Favored : 83.92 % Rotamer: Outliers : 3.51 % Allowed : 23.13 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.85 (0.30), residues: 765 helix: -0.25 (0.30), residues: 324 sheet: -1.95 (0.71), residues: 37 loop : -3.48 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.003 0.001 HIS A 582 PHE 0.028 0.001 PHE A 792 TYR 0.023 0.002 TYR A 496 ARG 0.006 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7572 (tpp) cc_final: 0.7270 (tpp) REVERT: A 92 ARG cc_start: 0.7273 (mtm110) cc_final: 0.7011 (mtm110) REVERT: A 119 LYS cc_start: 0.8637 (tppp) cc_final: 0.8257 (tppp) REVERT: A 148 MET cc_start: 0.6309 (tmm) cc_final: 0.6012 (tmm) REVERT: A 160 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 172 TYR cc_start: 0.6961 (m-80) cc_final: 0.6722 (m-80) REVERT: A 208 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6813 (mm-30) REVERT: A 223 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8118 (mtmm) REVERT: A 226 PHE cc_start: 0.8679 (t80) cc_final: 0.8342 (t80) REVERT: A 332 MET cc_start: 0.5179 (pmm) cc_final: 0.4792 (pmm) REVERT: A 408 ARG cc_start: 0.7712 (tmm-80) cc_final: 0.7357 (tmm-80) REVERT: A 441 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7980 (mm) REVERT: A 443 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8078 (mtmm) REVERT: A 457 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 532 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7486 (mm-30) REVERT: A 551 ASP cc_start: 0.7230 (t70) cc_final: 0.6838 (t70) REVERT: A 570 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7329 (t0) REVERT: A 590 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7241 (tpp80) REVERT: A 624 LYS cc_start: 0.8087 (tptm) cc_final: 0.7733 (tttm) REVERT: A 630 ILE cc_start: 0.8610 (tp) cc_final: 0.8319 (tp) REVERT: A 695 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 723 LYS cc_start: 0.8124 (tmtt) cc_final: 0.7694 (tmtt) REVERT: A 747 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8000 (mm) REVERT: A 766 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7938 (pp30) REVERT: A 778 GLN cc_start: 0.7976 (mp10) cc_final: 0.7757 (mp10) REVERT: A 812 LEU cc_start: 0.8349 (mt) cc_final: 0.8026 (mt) REVERT: A 814 GLN cc_start: 0.7960 (pp30) cc_final: 0.7506 (pp30) REVERT: A 865 LEU cc_start: 0.8570 (mm) cc_final: 0.8256 (mt) REVERT: A 867 LEU cc_start: 0.8932 (pp) cc_final: 0.8423 (pp) REVERT: A 871 PHE cc_start: 0.7304 (m-80) cc_final: 0.6914 (m-80) REVERT: A 873 TYR cc_start: 0.7328 (t80) cc_final: 0.6893 (t80) outliers start: 24 outliers final: 16 residues processed: 217 average time/residue: 0.2152 time to fit residues: 58.8141 Evaluate side-chains 228 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 911 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 45 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 863 HIS A 887 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6357 Z= 0.221 Angle : 0.745 13.056 8593 Z= 0.380 Chirality : 0.048 0.366 947 Planarity : 0.005 0.052 1089 Dihedral : 7.173 71.693 871 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.82 % Favored : 84.05 % Rotamer: Outliers : 3.95 % Allowed : 23.43 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.30), residues: 765 helix: -0.16 (0.30), residues: 318 sheet: -1.94 (0.71), residues: 37 loop : -3.44 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.003 0.001 HIS A 582 PHE 0.018 0.001 PHE A 629 TYR 0.020 0.002 TYR A 496 ARG 0.006 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7565 (tpp) cc_final: 0.7270 (tpp) REVERT: A 92 ARG cc_start: 0.7260 (mtm110) cc_final: 0.6985 (mtm110) REVERT: A 119 LYS cc_start: 0.8614 (tppp) cc_final: 0.8237 (tppp) REVERT: A 148 MET cc_start: 0.6220 (tmm) cc_final: 0.5930 (tmm) REVERT: A 160 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 172 TYR cc_start: 0.6885 (m-80) cc_final: 0.6595 (m-80) REVERT: A 208 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6744 (mm-30) REVERT: A 223 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8116 (mtmm) REVERT: A 225 GLU cc_start: 0.8049 (tp30) cc_final: 0.7832 (tp30) REVERT: A 226 PHE cc_start: 0.8676 (t80) cc_final: 0.8335 (t80) REVERT: A 262 GLU cc_start: 0.7071 (pm20) cc_final: 0.6632 (pm20) REVERT: A 332 MET cc_start: 0.5109 (pmm) cc_final: 0.4723 (pmm) REVERT: A 408 ARG cc_start: 0.7678 (tmm-80) cc_final: 0.7287 (tmm-80) REVERT: A 441 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7962 (mm) REVERT: A 457 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 532 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7463 (mm-30) REVERT: A 551 ASP cc_start: 0.7205 (t70) cc_final: 0.6803 (t70) REVERT: A 570 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7281 (t0) REVERT: A 585 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.8116 (mmm-85) REVERT: A 590 ARG cc_start: 0.7596 (tpp80) cc_final: 0.7225 (tpp80) REVERT: A 624 LYS cc_start: 0.8077 (tptm) cc_final: 0.7712 (tttm) REVERT: A 630 ILE cc_start: 0.8606 (tp) cc_final: 0.8306 (tp) REVERT: A 669 GLN cc_start: 0.8210 (tp40) cc_final: 0.8006 (tp40) REVERT: A 723 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7748 (tmtt) REVERT: A 747 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8007 (mm) REVERT: A 766 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7880 (pp30) REVERT: A 812 LEU cc_start: 0.8341 (mt) cc_final: 0.8011 (mt) REVERT: A 814 GLN cc_start: 0.7944 (pp30) cc_final: 0.7462 (pp30) REVERT: A 865 LEU cc_start: 0.8575 (mm) cc_final: 0.8262 (mt) REVERT: A 867 LEU cc_start: 0.8937 (pp) cc_final: 0.8440 (pp) REVERT: A 871 PHE cc_start: 0.7347 (m-80) cc_final: 0.6980 (m-80) REVERT: A 873 TYR cc_start: 0.7293 (t80) cc_final: 0.6888 (t80) outliers start: 27 outliers final: 20 residues processed: 219 average time/residue: 0.2171 time to fit residues: 59.5612 Evaluate side-chains 227 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 911 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A 887 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6357 Z= 0.230 Angle : 0.750 13.755 8593 Z= 0.383 Chirality : 0.048 0.404 947 Planarity : 0.005 0.052 1089 Dihedral : 7.148 70.089 871 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.08 % Favored : 83.79 % Rotamer: Outliers : 3.66 % Allowed : 24.74 % Favored : 71.60 % 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: -2.73 (0.30), residues: 765 helix: -0.05 (0.30), residues: 314 sheet: -1.87 (0.73), residues: 37 loop : -3.43 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.004 0.001 HIS A 811 PHE 0.017 0.001 PHE A 629 TYR 0.019 0.002 TYR A 496 ARG 0.006 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7563 (tpp) cc_final: 0.7274 (tpp) REVERT: A 62 LYS cc_start: 0.8301 (ttmm) cc_final: 0.8029 (mtmm) REVERT: A 92 ARG cc_start: 0.7239 (mtm110) cc_final: 0.6966 (mtm110) REVERT: A 119 LYS cc_start: 0.8616 (tppp) cc_final: 0.8238 (tppp) REVERT: A 148 MET cc_start: 0.6198 (tmm) cc_final: 0.5901 (tmm) REVERT: A 160 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7059 (tm-30) REVERT: A 172 TYR cc_start: 0.7067 (m-80) cc_final: 0.6728 (m-80) REVERT: A 208 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6767 (mm-30) REVERT: A 223 LYS cc_start: 0.8341 (mtmm) cc_final: 0.8116 (mtmm) REVERT: A 225 GLU cc_start: 0.8043 (tp30) cc_final: 0.7832 (tp30) REVERT: A 226 PHE cc_start: 0.8681 (t80) cc_final: 0.8343 (t80) REVERT: A 260 ARG cc_start: 0.6619 (mpp-170) cc_final: 0.6349 (mpp-170) REVERT: A 332 MET cc_start: 0.5090 (pmm) cc_final: 0.4718 (pmm) REVERT: A 408 ARG cc_start: 0.7683 (tmm-80) cc_final: 0.7271 (tmm-80) REVERT: A 409 ASP cc_start: 0.7532 (t0) cc_final: 0.7263 (t0) REVERT: A 441 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7977 (mm) REVERT: A 443 LYS cc_start: 0.8454 (mtmm) cc_final: 0.7875 (mtmm) REVERT: A 457 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7831 (tm-30) REVERT: A 532 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 551 ASP cc_start: 0.7103 (t70) cc_final: 0.6716 (t70) REVERT: A 585 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: A 590 ARG cc_start: 0.7615 (tpp80) cc_final: 0.7259 (tpp80) REVERT: A 624 LYS cc_start: 0.8078 (tptm) cc_final: 0.7723 (tttm) REVERT: A 630 ILE cc_start: 0.8610 (tp) cc_final: 0.8316 (tp) REVERT: A 669 GLN cc_start: 0.8212 (tp40) cc_final: 0.8010 (tp40) REVERT: A 766 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7832 (pp30) REVERT: A 808 VAL cc_start: 0.8495 (p) cc_final: 0.8148 (t) REVERT: A 812 LEU cc_start: 0.8347 (mt) cc_final: 0.8042 (mt) REVERT: A 814 GLN cc_start: 0.7944 (pp30) cc_final: 0.7450 (pp30) REVERT: A 865 LEU cc_start: 0.8587 (mm) cc_final: 0.8267 (mt) REVERT: A 867 LEU cc_start: 0.8954 (pp) cc_final: 0.8462 (pp) REVERT: A 871 PHE cc_start: 0.7359 (m-80) cc_final: 0.7007 (m-80) REVERT: A 873 TYR cc_start: 0.7271 (t80) cc_final: 0.6844 (t80) outliers start: 25 outliers final: 22 residues processed: 212 average time/residue: 0.2127 time to fit residues: 56.4065 Evaluate side-chains 222 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 199 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 911 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 62 optimal weight: 0.0040 chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 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 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 887 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6357 Z= 0.229 Angle : 0.763 14.003 8593 Z= 0.388 Chirality : 0.048 0.418 947 Planarity : 0.005 0.050 1089 Dihedral : 7.092 69.923 871 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.56 % Favored : 84.31 % Rotamer: Outliers : 3.51 % Allowed : 25.48 % Favored : 71.01 % 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: -2.72 (0.30), residues: 765 helix: -0.10 (0.30), residues: 318 sheet: -1.85 (0.74), residues: 37 loop : -3.40 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS A 582 PHE 0.017 0.001 PHE A 629 TYR 0.019 0.002 TYR A 496 ARG 0.006 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7551 (tpp) cc_final: 0.7310 (tpp) REVERT: A 62 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7572 (mtmm) REVERT: A 92 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6941 (mtm110) REVERT: A 119 LYS cc_start: 0.8593 (tppp) cc_final: 0.8218 (tppp) REVERT: A 148 MET cc_start: 0.6154 (tmm) cc_final: 0.5863 (tmm) REVERT: A 160 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7054 (tm-30) REVERT: A 166 PHE cc_start: 0.8594 (m-10) cc_final: 0.8228 (m-80) REVERT: A 168 ASP cc_start: 0.7709 (p0) cc_final: 0.7112 (p0) REVERT: A 172 TYR cc_start: 0.7066 (m-80) cc_final: 0.6745 (m-80) REVERT: A 208 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6659 (mm-30) REVERT: A 223 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8111 (mtmm) REVERT: A 225 GLU cc_start: 0.8028 (tp30) cc_final: 0.7825 (tp30) REVERT: A 226 PHE cc_start: 0.8674 (t80) cc_final: 0.8320 (t80) REVERT: A 332 MET cc_start: 0.4883 (pmm) cc_final: 0.4525 (pmm) REVERT: A 401 ARG cc_start: 0.5451 (pmt-80) cc_final: 0.4865 (mmp80) REVERT: A 408 ARG cc_start: 0.7634 (tmm-80) cc_final: 0.7310 (tmm-80) REVERT: A 441 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7969 (mm) REVERT: A 443 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7873 (mtmm) REVERT: A 457 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 532 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7418 (mm-30) REVERT: A 541 GLN cc_start: 0.7296 (pt0) cc_final: 0.6820 (pt0) REVERT: A 551 ASP cc_start: 0.7099 (t70) cc_final: 0.6714 (t70) REVERT: A 570 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7399 (t0) REVERT: A 624 LYS cc_start: 0.8062 (tptm) cc_final: 0.7698 (tttm) REVERT: A 630 ILE cc_start: 0.8613 (tp) cc_final: 0.8313 (tp) REVERT: A 669 GLN cc_start: 0.8209 (tp40) cc_final: 0.8002 (tp40) REVERT: A 766 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7925 (pp30) REVERT: A 778 GLN cc_start: 0.8062 (mp10) cc_final: 0.7806 (mp10) REVERT: A 808 VAL cc_start: 0.8514 (p) cc_final: 0.8162 (t) REVERT: A 812 LEU cc_start: 0.8332 (mt) cc_final: 0.8027 (mt) REVERT: A 814 GLN cc_start: 0.7928 (pp30) cc_final: 0.7428 (pp30) REVERT: A 865 LEU cc_start: 0.8568 (mm) cc_final: 0.8275 (mt) REVERT: A 867 LEU cc_start: 0.8958 (pp) cc_final: 0.8469 (pp) REVERT: A 871 PHE cc_start: 0.7348 (m-80) cc_final: 0.7009 (m-80) REVERT: A 873 TYR cc_start: 0.7232 (t80) cc_final: 0.6830 (t80) outliers start: 24 outliers final: 17 residues processed: 209 average time/residue: 0.2242 time to fit residues: 59.1702 Evaluate side-chains 223 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 911 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 0.0270 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 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 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6357 Z= 0.230 Angle : 0.780 13.761 8593 Z= 0.398 Chirality : 0.048 0.414 947 Planarity : 0.005 0.050 1089 Dihedral : 7.079 69.306 871 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.56 % Favored : 84.31 % Rotamer: Outliers : 2.93 % Allowed : 26.35 % Favored : 70.72 % 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: -2.67 (0.30), residues: 765 helix: -0.02 (0.30), residues: 314 sheet: -1.90 (0.74), residues: 37 loop : -3.37 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.003 0.001 HIS A 582 PHE 0.017 0.001 PHE A 629 TYR 0.018 0.002 TYR A 496 ARG 0.007 0.001 ARG A 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7575 (tpp) cc_final: 0.7336 (tpp) REVERT: A 62 LYS cc_start: 0.8273 (ttmm) cc_final: 0.7533 (mtmm) REVERT: A 87 TYR cc_start: 0.8220 (p90) cc_final: 0.7844 (p90) REVERT: A 92 ARG cc_start: 0.7222 (mtm110) cc_final: 0.6943 (mtm110) REVERT: A 119 LYS cc_start: 0.8595 (tppp) cc_final: 0.8207 (tppp) REVERT: A 148 MET cc_start: 0.6140 (tmm) cc_final: 0.5892 (tmm) REVERT: A 158 GLU cc_start: 0.7444 (tp30) cc_final: 0.7057 (tp30) REVERT: A 160 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7049 (tm-30) REVERT: A 166 PHE cc_start: 0.8612 (m-10) cc_final: 0.8239 (m-80) REVERT: A 168 ASP cc_start: 0.7687 (p0) cc_final: 0.7099 (p0) REVERT: A 172 TYR cc_start: 0.7056 (m-80) cc_final: 0.6726 (m-80) REVERT: A 208 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6648 (mm-30) REVERT: A 223 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8113 (mtmm) REVERT: A 225 GLU cc_start: 0.8026 (tp30) cc_final: 0.7813 (tp30) REVERT: A 226 PHE cc_start: 0.8660 (t80) cc_final: 0.8288 (t80) REVERT: A 262 GLU cc_start: 0.7146 (pm20) cc_final: 0.6852 (pm20) REVERT: A 332 MET cc_start: 0.4880 (pmm) cc_final: 0.4511 (pmm) REVERT: A 401 ARG cc_start: 0.5442 (pmt-80) cc_final: 0.4890 (mmp80) REVERT: A 408 ARG cc_start: 0.7633 (tmm-80) cc_final: 0.7336 (tmm-80) REVERT: A 409 ASP cc_start: 0.7492 (t0) cc_final: 0.7237 (t0) REVERT: A 441 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7979 (mm) REVERT: A 443 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8141 (mtmm) REVERT: A 457 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 532 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 541 GLN cc_start: 0.7289 (pt0) cc_final: 0.6828 (pt0) REVERT: A 551 ASP cc_start: 0.7094 (t70) cc_final: 0.6709 (t70) REVERT: A 624 LYS cc_start: 0.8056 (tptm) cc_final: 0.7693 (tttm) REVERT: A 630 ILE cc_start: 0.8607 (tp) cc_final: 0.8310 (tp) REVERT: A 669 GLN cc_start: 0.8206 (tp40) cc_final: 0.7997 (tp40) REVERT: A 709 ASN cc_start: 0.7621 (p0) cc_final: 0.6933 (p0) REVERT: A 712 ASP cc_start: 0.8098 (m-30) cc_final: 0.7813 (m-30) REVERT: A 766 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7949 (pp30) REVERT: A 778 GLN cc_start: 0.8105 (mp10) cc_final: 0.7830 (mp10) REVERT: A 808 VAL cc_start: 0.8516 (p) cc_final: 0.8174 (t) REVERT: A 812 LEU cc_start: 0.8334 (mt) cc_final: 0.8033 (mt) REVERT: A 814 GLN cc_start: 0.7927 (pp30) cc_final: 0.7411 (pp30) REVERT: A 865 LEU cc_start: 0.8566 (mm) cc_final: 0.8273 (mt) REVERT: A 867 LEU cc_start: 0.8957 (pp) cc_final: 0.8469 (pp) REVERT: A 871 PHE cc_start: 0.7340 (m-80) cc_final: 0.7006 (m-80) REVERT: A 873 TYR cc_start: 0.7217 (t80) cc_final: 0.6848 (t80) outliers start: 20 outliers final: 18 residues processed: 211 average time/residue: 0.2163 time to fit residues: 57.4253 Evaluate side-chains 219 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 911 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.0000 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 887 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.157040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.139260 restraints weight = 10327.996| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.66 r_work: 0.3735 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6357 Z= 0.222 Angle : 0.776 13.515 8593 Z= 0.395 Chirality : 0.048 0.409 947 Planarity : 0.005 0.057 1089 Dihedral : 7.033 69.180 871 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.42 % Favored : 84.44 % Rotamer: Outliers : 3.07 % Allowed : 26.50 % Favored : 70.42 % 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: -2.66 (0.30), residues: 765 helix: -0.09 (0.30), residues: 320 sheet: -1.96 (0.73), residues: 37 loop : -3.32 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.004 0.001 HIS A 253 PHE 0.017 0.001 PHE A 629 TYR 0.049 0.002 TYR A 496 ARG 0.007 0.001 ARG A 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.52 seconds wall clock time: 35 minutes 39.51 seconds (2139.51 seconds total)