Starting phenix.real_space_refine on Tue Mar 11 16:54:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rav_24387/03_2025/7rav_24387.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rav_24387/03_2025/7rav_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/cci-nas-00/data/ceres_data/7rav_24387/03_2025/7rav_24387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rav_24387/03_2025/7rav_24387.map" model { file = "/net/cci-nas-00/data/ceres_data/7rav_24387/03_2025/7rav_24387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rav_24387/03_2025/7rav_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-5624/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: 4.39, per 1000 atoms: 0.71 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: 1.56 Conformation dependent library (CDL) restraints added in 993.4 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: 0.64 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: 1.68 Time building geometry restraints manager: 1.81 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.760 Find NCS groups from input model: 0.070 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 8 poor density : 225 time to evaluate : 0.740 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: 0.2141 time to fit residues: 61.4862 Evaluate side-chains 198 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.155214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.137636 restraints weight = 10334.523| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.68 r_work: 0.3720 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 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 to be fit. rotamer outliers: 10 poor density : 216 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7645 (tpp) cc_final: 0.7310 (tpp) REVERT: A 57 MET cc_start: 0.8559 (ptp) cc_final: 0.8335 (ptp) REVERT: A 62 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8254 (mtmm) REVERT: A 138 TYR cc_start: 0.7089 (t80) cc_final: 0.6751 (t80) REVERT: A 148 MET cc_start: 0.6929 (tmm) cc_final: 0.6585 (tmm) REVERT: A 160 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7720 (tm-30) REVERT: A 164 GLU cc_start: 0.8031 (pp20) cc_final: 0.7551 (pp20) REVERT: A 167 GLU cc_start: 0.7946 (mp0) cc_final: 0.7313 (mp0) REVERT: A 223 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8375 (mtmm) REVERT: A 332 MET cc_start: 0.6010 (pmm) cc_final: 0.5466 (pmm) REVERT: A 408 ARG cc_start: 0.8204 (tmm-80) cc_final: 0.7693 (tmm-80) REVERT: A 423 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 443 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8039 (mtmm) REVERT: A 454 THR cc_start: 0.8372 (p) cc_final: 0.7972 (t) REVERT: A 455 ILE cc_start: 0.8465 (mm) cc_final: 0.7981 (tp) REVERT: A 457 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 551 ASP cc_start: 0.7626 (t70) cc_final: 0.6934 (t0) REVERT: A 570 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7578 (t0) REVERT: A 630 ILE cc_start: 0.8740 (tp) cc_final: 0.8424 (tp) REVERT: A 766 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7851 (pp30) REVERT: A 812 LEU cc_start: 0.8686 (mt) cc_final: 0.8379 (mt) REVERT: A 814 GLN cc_start: 0.8149 (pp30) cc_final: 0.7748 (pp30) REVERT: A 863 HIS cc_start: 0.8010 (m90) cc_final: 0.7230 (m90) REVERT: A 865 LEU cc_start: 0.8625 (mm) cc_final: 0.8392 (mm) REVERT: A 867 LEU cc_start: 0.9057 (pp) cc_final: 0.8573 (pp) REVERT: A 871 PHE cc_start: 0.7737 (m-80) cc_final: 0.7246 (m-80) REVERT: A 873 TYR cc_start: 0.7717 (t80) cc_final: 0.7294 (t80) outliers start: 10 outliers final: 7 residues processed: 219 average time/residue: 0.2189 time to fit residues: 60.0018 Evaluate side-chains 206 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 570 ASN 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 9 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.0370 chunk 16 optimal weight: 0.4980 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.157667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140311 restraints weight = 10426.221| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.61 r_work: 0.3748 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1939 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= 0.193 Angle : 0.716 8.888 8593 Z= 0.372 Chirality : 0.045 0.167 947 Planarity : 0.005 0.057 1089 Dihedral : 7.441 81.583 871 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.16 % Favored : 84.58 % Rotamer: Outliers : 2.20 % Allowed : 18.45 % Favored : 79.36 % 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: -2.93 (0.30), residues: 765 helix: -0.24 (0.31), residues: 317 sheet: -1.93 (0.72), residues: 37 loop : -3.54 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.005 0.001 HIS A 811 PHE 0.036 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 217 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.651 Fit side-chains REVERT: A 47 MET cc_start: 0.7647 (tpp) cc_final: 0.7339 (tpp) REVERT: A 62 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8225 (mtmm) REVERT: A 92 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7646 (mtm110) REVERT: A 148 MET cc_start: 0.6896 (tmm) cc_final: 0.6539 (tmm) REVERT: A 160 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7551 (tm-30) REVERT: A 164 GLU cc_start: 0.8027 (pp20) cc_final: 0.7669 (pp20) REVERT: A 167 GLU cc_start: 0.7854 (mp0) cc_final: 0.7343 (mp0) REVERT: A 172 TYR cc_start: 0.7199 (m-80) cc_final: 0.6987 (m-80) REVERT: A 208 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7192 (mm-30) REVERT: A 223 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8346 (mtmm) REVERT: A 226 PHE cc_start: 0.8739 (t80) cc_final: 0.8095 (t80) REVERT: A 282 MET cc_start: 0.7017 (tpt) cc_final: 0.6722 (tpt) REVERT: A 332 MET cc_start: 0.5989 (pmm) cc_final: 0.5413 (pmm) REVERT: A 408 ARG cc_start: 0.8137 (tmm-80) cc_final: 0.7715 (tmm-80) REVERT: A 423 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 443 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8017 (mtmm) REVERT: A 454 THR cc_start: 0.8299 (p) cc_final: 0.7986 (t) REVERT: A 455 ILE cc_start: 0.8499 (mm) cc_final: 0.8038 (tp) REVERT: A 457 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7894 (tm-30) REVERT: A 551 ASP cc_start: 0.7580 (t70) cc_final: 0.6915 (t0) REVERT: A 585 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.8520 (mmm-85) REVERT: A 624 LYS cc_start: 0.8046 (tptm) cc_final: 0.7679 (tttm) REVERT: A 630 ILE cc_start: 0.8698 (tp) cc_final: 0.8406 (tp) REVERT: A 652 TRP cc_start: 0.6147 (t60) cc_final: 0.5905 (t60) REVERT: A 712 ASP cc_start: 0.8411 (m-30) cc_final: 0.8040 (m-30) REVERT: A 723 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7519 (tmtt) REVERT: A 766 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7954 (pp30) REVERT: A 778 GLN cc_start: 0.8125 (mp10) cc_final: 0.7925 (mp10) REVERT: A 812 LEU cc_start: 0.8619 (mt) cc_final: 0.8336 (mt) REVERT: A 814 GLN cc_start: 0.8155 (pp30) cc_final: 0.7734 (pp30) REVERT: A 863 HIS cc_start: 0.7957 (m90) cc_final: 0.7230 (m90) REVERT: A 865 LEU cc_start: 0.8580 (mm) cc_final: 0.8357 (mm) REVERT: A 867 LEU cc_start: 0.9006 (pp) cc_final: 0.8511 (pp) REVERT: A 871 PHE cc_start: 0.7736 (m-80) cc_final: 0.7278 (m-80) REVERT: A 873 TYR cc_start: 0.7685 (t80) cc_final: 0.7230 (t80) outliers start: 15 outliers final: 11 residues processed: 208 average time/residue: 0.2138 time to fit residues: 55.9716 Evaluate side-chains 210 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.0970 chunk 53 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 570 ASN A 606 ASN A 900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.158893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.141497 restraints weight = 10491.919| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.67 r_work: 0.3756 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6357 Z= 0.179 Angle : 0.695 8.670 8593 Z= 0.358 Chirality : 0.045 0.199 947 Planarity : 0.004 0.056 1089 Dihedral : 7.180 80.132 871 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.51 % Favored : 85.36 % Rotamer: Outliers : 2.93 % Allowed : 20.50 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.30), residues: 765 helix: -0.07 (0.31), residues: 313 sheet: -1.91 (0.70), residues: 37 loop : -3.44 (0.28), residues: 415 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 0.037 0.001 PHE A 792 TYR 0.030 0.002 TYR A 496 ARG 0.005 0.001 ARG A 74 *********************** 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 226 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.736 Fit side-chains REVERT: A 47 MET cc_start: 0.7674 (tpp) cc_final: 0.7390 (tpp) REVERT: A 62 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8221 (mtmm) REVERT: A 92 ARG cc_start: 0.7805 (mtm110) cc_final: 0.7560 (mtm110) REVERT: A 119 LYS cc_start: 0.8900 (tppp) cc_final: 0.8474 (tppp) REVERT: A 148 MET cc_start: 0.6879 (tmm) cc_final: 0.6493 (tmm) REVERT: A 160 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7635 (tm-30) REVERT: A 172 TYR cc_start: 0.7192 (m-80) cc_final: 0.6949 (m-80) REVERT: A 208 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7284 (mm-30) REVERT: A 223 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8357 (mtmm) REVERT: A 226 PHE cc_start: 0.8705 (t80) cc_final: 0.8279 (t80) REVERT: A 282 MET cc_start: 0.7091 (tpt) cc_final: 0.6759 (tpt) REVERT: A 332 MET cc_start: 0.5971 (pmm) cc_final: 0.5362 (pmm) REVERT: A 408 ARG cc_start: 0.8103 (tmm-80) cc_final: 0.7739 (tmm-80) REVERT: A 409 ASP cc_start: 0.7860 (t0) cc_final: 0.7567 (t0) REVERT: A 423 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7614 (mm-30) REVERT: A 443 LYS cc_start: 0.8438 (mtmm) cc_final: 0.7819 (mtmm) REVERT: A 454 THR cc_start: 0.8260 (p) cc_final: 0.8028 (t) REVERT: A 455 ILE cc_start: 0.8525 (mm) cc_final: 0.8063 (tp) REVERT: A 457 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 532 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 551 ASP cc_start: 0.7545 (t70) cc_final: 0.6919 (t0) REVERT: A 570 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7327 (t0) REVERT: A 624 LYS cc_start: 0.8057 (tptm) cc_final: 0.7678 (tttm) REVERT: A 630 ILE cc_start: 0.8664 (tp) cc_final: 0.8395 (tp) REVERT: A 712 ASP cc_start: 0.8372 (m-30) cc_final: 0.7973 (m-30) REVERT: A 723 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7499 (tmtt) REVERT: A 766 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 812 LEU cc_start: 0.8599 (mt) cc_final: 0.8309 (mt) REVERT: A 814 GLN cc_start: 0.8147 (pp30) cc_final: 0.7723 (pp30) REVERT: A 863 HIS cc_start: 0.8081 (m90) cc_final: 0.7344 (m90) REVERT: A 865 LEU cc_start: 0.8653 (mm) cc_final: 0.8320 (mt) REVERT: A 867 LEU cc_start: 0.9023 (pp) cc_final: 0.8545 (pp) REVERT: A 871 PHE cc_start: 0.7743 (m-80) cc_final: 0.7302 (m-80) REVERT: A 873 TYR cc_start: 0.7673 (t80) cc_final: 0.7218 (t80) outliers start: 20 outliers final: 13 residues processed: 215 average time/residue: 0.2214 time to fit residues: 59.9688 Evaluate side-chains 216 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET 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 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 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 28 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 606 ASN A 887 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.157602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140150 restraints weight = 10382.492| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.60 r_work: 0.3737 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2368 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= 0.223 Angle : 0.715 10.944 8593 Z= 0.368 Chirality : 0.047 0.319 947 Planarity : 0.005 0.054 1089 Dihedral : 7.166 75.279 871 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.03 % Favored : 84.84 % Rotamer: Outliers : 3.07 % Allowed : 21.82 % Favored : 75.11 % 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: -2.77 (0.30), residues: 765 helix: -0.10 (0.30), residues: 314 sheet: -1.96 (0.69), residues: 37 loop : -3.43 (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 811 PHE 0.028 0.001 PHE A 792 TYR 0.025 0.002 TYR A 496 ARG 0.005 0.001 ARG A 74 *********************** 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 220 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7675 (tpp) cc_final: 0.7409 (tpp) REVERT: A 79 GLN cc_start: 0.8212 (mp10) cc_final: 0.7946 (mm-40) REVERT: A 92 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7670 (mtm110) REVERT: A 119 LYS cc_start: 0.8875 (tppp) cc_final: 0.8477 (tppp) REVERT: A 148 MET cc_start: 0.6916 (tmm) cc_final: 0.6517 (tmm) REVERT: A 158 GLU cc_start: 0.7591 (tp30) cc_final: 0.7340 (tp30) REVERT: A 167 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 172 TYR cc_start: 0.7413 (m-80) cc_final: 0.7101 (m-80) REVERT: A 208 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 223 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8354 (mtmm) REVERT: A 226 PHE cc_start: 0.8699 (t80) cc_final: 0.8264 (t80) REVERT: A 282 MET cc_start: 0.7119 (tpt) cc_final: 0.6806 (tpt) REVERT: A 332 MET cc_start: 0.5740 (pmm) cc_final: 0.5211 (pmm) REVERT: A 408 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7798 (tmm-80) REVERT: A 454 THR cc_start: 0.8225 (p) cc_final: 0.8019 (t) REVERT: A 455 ILE cc_start: 0.8583 (mm) cc_final: 0.8126 (tp) REVERT: A 457 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 532 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 551 ASP cc_start: 0.7647 (t70) cc_final: 0.7139 (t70) REVERT: A 570 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7238 (t0) REVERT: A 590 ARG cc_start: 0.8220 (tpp-160) cc_final: 0.7999 (tpp80) REVERT: A 624 LYS cc_start: 0.8135 (tptm) cc_final: 0.7743 (tttm) REVERT: A 630 ILE cc_start: 0.8632 (tp) cc_final: 0.8360 (tp) REVERT: A 723 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7579 (tmtt) REVERT: A 766 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 812 LEU cc_start: 0.8599 (mt) cc_final: 0.8311 (mt) REVERT: A 814 GLN cc_start: 0.8235 (pp30) cc_final: 0.7775 (pp30) REVERT: A 865 LEU cc_start: 0.8649 (mm) cc_final: 0.8323 (mt) REVERT: A 867 LEU cc_start: 0.9029 (pp) cc_final: 0.8570 (pp) REVERT: A 871 PHE cc_start: 0.7761 (m-80) cc_final: 0.7391 (m-80) REVERT: A 873 TYR cc_start: 0.7574 (t80) cc_final: 0.7139 (t80) outliers start: 21 outliers final: 14 residues processed: 206 average time/residue: 0.2259 time to fit residues: 58.8926 Evaluate side-chains 213 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 59 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.0000 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.3582 ------------------------------------------------------------------------------- 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 A 900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.158414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140926 restraints weight = 10318.008| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.60 r_work: 0.3749 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6357 Z= 0.189 Angle : 0.712 12.528 8593 Z= 0.363 Chirality : 0.046 0.395 947 Planarity : 0.004 0.053 1089 Dihedral : 7.026 74.950 871 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.69 % Favored : 84.18 % Rotamer: Outliers : 3.51 % Allowed : 21.96 % Favored : 74.52 % 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: -2.64 (0.30), residues: 765 helix: 0.02 (0.30), residues: 310 sheet: -1.98 (0.70), residues: 37 loop : -3.33 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.004 0.001 HIS A 582 PHE 0.022 0.001 PHE A 792 TYR 0.020 0.002 TYR A 496 ARG 0.004 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 230 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7676 (tpp) cc_final: 0.7425 (tpp) REVERT: A 79 GLN cc_start: 0.8215 (mp10) cc_final: 0.7951 (mm-40) REVERT: A 119 LYS cc_start: 0.8817 (tppp) cc_final: 0.8418 (tppp) REVERT: A 138 TYR cc_start: 0.6741 (t80) cc_final: 0.6411 (t80) REVERT: A 148 MET cc_start: 0.6827 (tmm) cc_final: 0.6436 (tmm) REVERT: A 158 GLU cc_start: 0.7559 (tp30) cc_final: 0.7299 (tp30) REVERT: A 167 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 172 TYR cc_start: 0.7422 (m-80) cc_final: 0.7067 (m-80) REVERT: A 206 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8200 (m110) REVERT: A 208 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 223 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8384 (mtmm) REVERT: A 226 PHE cc_start: 0.8688 (t80) cc_final: 0.8330 (t80) REVERT: A 260 ARG cc_start: 0.7070 (mpp-170) cc_final: 0.6855 (mpp-170) REVERT: A 282 MET cc_start: 0.7175 (tpt) cc_final: 0.6848 (tpt) REVERT: A 332 MET cc_start: 0.5469 (pmm) cc_final: 0.4965 (pmm) REVERT: A 408 ARG cc_start: 0.8133 (tmm-80) cc_final: 0.7743 (tmm-80) REVERT: A 409 ASP cc_start: 0.7875 (t0) cc_final: 0.7597 (t0) REVERT: A 443 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8187 (mtmm) REVERT: A 455 ILE cc_start: 0.8575 (mm) cc_final: 0.8124 (tp) REVERT: A 457 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 532 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 551 ASP cc_start: 0.7574 (t70) cc_final: 0.7068 (t70) REVERT: A 590 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.8006 (tpp80) REVERT: A 624 LYS cc_start: 0.8108 (tptm) cc_final: 0.7718 (tttm) REVERT: A 630 ILE cc_start: 0.8624 (tp) cc_final: 0.8359 (tp) REVERT: A 674 TYR cc_start: 0.8429 (t80) cc_final: 0.8191 (t80) REVERT: A 709 ASN cc_start: 0.7770 (p0) cc_final: 0.7129 (p0) REVERT: A 712 ASP cc_start: 0.8327 (m-30) cc_final: 0.8017 (m-30) REVERT: A 723 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7571 (tmtt) REVERT: A 766 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 812 LEU cc_start: 0.8596 (mt) cc_final: 0.8304 (mt) REVERT: A 814 GLN cc_start: 0.8197 (pp30) cc_final: 0.7726 (pp30) REVERT: A 865 LEU cc_start: 0.8654 (mm) cc_final: 0.8327 (mt) REVERT: A 867 LEU cc_start: 0.9044 (pp) cc_final: 0.8597 (pp) REVERT: A 871 PHE cc_start: 0.7815 (m-80) cc_final: 0.7459 (m-80) REVERT: A 873 TYR cc_start: 0.7508 (t80) cc_final: 0.7076 (t80) outliers start: 24 outliers final: 18 residues processed: 217 average time/residue: 0.2093 time to fit residues: 57.1274 Evaluate side-chains 218 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 570 ASN A 863 HIS A 887 GLN A 900 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.157845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140355 restraints weight = 10331.321| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.59 r_work: 0.3743 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2582 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= 0.227 Angle : 0.748 13.239 8593 Z= 0.380 Chirality : 0.048 0.399 947 Planarity : 0.005 0.056 1089 Dihedral : 7.023 72.073 871 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.42 % Favored : 84.44 % Rotamer: Outliers : 3.81 % Allowed : 23.13 % Favored : 73.06 % 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: -2.63 (0.30), residues: 765 helix: 0.00 (0.30), residues: 311 sheet: -1.88 (0.73), residues: 37 loop : -3.31 (0.29), residues: 417 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 0.022 0.001 PHE A 708 TYR 0.047 0.002 TYR A 496 ARG 0.005 0.001 ARG A 92 *********************** 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 230 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7670 (tpp) cc_final: 0.7413 (tpp) REVERT: A 92 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7559 (mtm110) REVERT: A 119 LYS cc_start: 0.8825 (tppp) cc_final: 0.8430 (tppp) REVERT: A 148 MET cc_start: 0.6838 (tmm) cc_final: 0.6456 (tmm) REVERT: A 158 GLU cc_start: 0.7650 (tp30) cc_final: 0.7410 (tp30) REVERT: A 172 TYR cc_start: 0.7422 (m-80) cc_final: 0.7068 (m-80) REVERT: A 208 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 223 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8370 (mtmm) REVERT: A 226 PHE cc_start: 0.8714 (t80) cc_final: 0.8281 (t80) REVERT: A 262 GLU cc_start: 0.7504 (pm20) cc_final: 0.7024 (pm20) REVERT: A 282 MET cc_start: 0.7302 (tpt) cc_final: 0.6933 (tpt) REVERT: A 332 MET cc_start: 0.5525 (pmm) cc_final: 0.5024 (pmm) REVERT: A 408 ARG cc_start: 0.8143 (tmm-80) cc_final: 0.7776 (tmm-80) REVERT: A 409 ASP cc_start: 0.7810 (t0) cc_final: 0.7543 (t0) REVERT: A 443 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8141 (mtmm) REVERT: A 457 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 532 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 551 ASP cc_start: 0.7536 (t70) cc_final: 0.7038 (t70) REVERT: A 570 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7290 (t0) REVERT: A 590 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7954 (tpp80) REVERT: A 624 LYS cc_start: 0.8121 (tptm) cc_final: 0.7727 (tttm) REVERT: A 630 ILE cc_start: 0.8657 (tp) cc_final: 0.8385 (tp) REVERT: A 695 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 723 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7718 (tmtt) REVERT: A 766 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8077 (tm-30) REVERT: A 812 LEU cc_start: 0.8591 (mt) cc_final: 0.8307 (mt) REVERT: A 814 GLN cc_start: 0.8205 (pp30) cc_final: 0.7716 (pp30) REVERT: A 865 LEU cc_start: 0.8701 (mm) cc_final: 0.8374 (mt) REVERT: A 867 LEU cc_start: 0.9065 (pp) cc_final: 0.8627 (pp) REVERT: A 871 PHE cc_start: 0.7798 (m-80) cc_final: 0.7443 (m-80) REVERT: A 873 TYR cc_start: 0.7494 (t80) cc_final: 0.7070 (t80) outliers start: 26 outliers final: 17 residues processed: 216 average time/residue: 0.2193 time to fit residues: 59.1791 Evaluate side-chains 215 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 300 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.0010 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.158241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140721 restraints weight = 10286.965| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.59 r_work: 0.3744 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6357 Z= 0.208 Angle : 0.754 13.847 8593 Z= 0.381 Chirality : 0.048 0.411 947 Planarity : 0.005 0.063 1089 Dihedral : 6.967 71.948 871 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.16 % Favored : 84.71 % Rotamer: Outliers : 3.37 % Allowed : 24.74 % Favored : 71.89 % 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: -2.58 (0.30), residues: 765 helix: 0.05 (0.30), residues: 310 sheet: -1.93 (0.72), residues: 37 loop : -3.27 (0.29), residues: 418 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 0.021 0.001 PHE A 708 TYR 0.048 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 226 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7657 (tpp) cc_final: 0.7405 (tpp) REVERT: A 92 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7453 (mtm110) REVERT: A 119 LYS cc_start: 0.8815 (tppp) cc_final: 0.8411 (tppp) REVERT: A 148 MET cc_start: 0.6793 (tmm) cc_final: 0.6397 (tmm) REVERT: A 158 GLU cc_start: 0.7667 (tp30) cc_final: 0.7426 (tp30) REVERT: A 172 TYR cc_start: 0.7454 (m-80) cc_final: 0.7074 (m-80) REVERT: A 208 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 223 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8466 (mtmm) REVERT: A 226 PHE cc_start: 0.8707 (t80) cc_final: 0.8316 (t80) REVERT: A 262 GLU cc_start: 0.7524 (pm20) cc_final: 0.7235 (pm20) REVERT: A 282 MET cc_start: 0.7291 (tpt) cc_final: 0.6895 (tpt) REVERT: A 332 MET cc_start: 0.5536 (pmm) cc_final: 0.5001 (pmm) REVERT: A 408 ARG cc_start: 0.8134 (tmm-80) cc_final: 0.7736 (tmm-80) REVERT: A 409 ASP cc_start: 0.7829 (t0) cc_final: 0.7577 (t0) REVERT: A 441 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8165 (mm) REVERT: A 443 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8297 (mtmm) REVERT: A 455 ILE cc_start: 0.8521 (mm) cc_final: 0.8191 (tp) REVERT: A 457 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 532 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 551 ASP cc_start: 0.7497 (t70) cc_final: 0.6994 (t70) REVERT: A 585 ARG cc_start: 0.8801 (mmm-85) cc_final: 0.8395 (mmm-85) REVERT: A 598 GLU cc_start: 0.7606 (tt0) cc_final: 0.7368 (tt0) REVERT: A 624 LYS cc_start: 0.8102 (tptm) cc_final: 0.7697 (tttm) REVERT: A 630 ILE cc_start: 0.8652 (tp) cc_final: 0.8387 (tp) REVERT: A 674 TYR cc_start: 0.8422 (t80) cc_final: 0.8179 (t80) REVERT: A 695 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 696 LEU cc_start: 0.8631 (tt) cc_final: 0.8429 (tp) REVERT: A 712 ASP cc_start: 0.8326 (m-30) cc_final: 0.7910 (m-30) REVERT: A 723 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7696 (tmtt) REVERT: A 766 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8221 (tm-30) REVERT: A 808 VAL cc_start: 0.8795 (p) cc_final: 0.8418 (t) REVERT: A 812 LEU cc_start: 0.8574 (mt) cc_final: 0.8295 (mt) REVERT: A 814 GLN cc_start: 0.8195 (pp30) cc_final: 0.7701 (pp30) REVERT: A 865 LEU cc_start: 0.8713 (mm) cc_final: 0.8385 (mt) REVERT: A 867 LEU cc_start: 0.9067 (pp) cc_final: 0.8633 (pp) REVERT: A 871 PHE cc_start: 0.7798 (m-80) cc_final: 0.7448 (m-80) REVERT: A 873 TYR cc_start: 0.7452 (t80) cc_final: 0.7052 (t80) outliers start: 23 outliers final: 18 residues processed: 215 average time/residue: 0.2157 time to fit residues: 58.5008 Evaluate side-chains 215 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 900 ASN 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 44 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 59 optimal weight: 0.3980 chunk 31 optimal weight: 0.0970 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 887 GLN A 900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.159676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.142213 restraints weight = 10394.189| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.61 r_work: 0.3771 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6357 Z= 0.187 Angle : 0.755 14.491 8593 Z= 0.379 Chirality : 0.047 0.412 947 Planarity : 0.005 0.043 1089 Dihedral : 6.871 72.806 871 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.51 % Favored : 85.36 % Rotamer: Outliers : 3.22 % Allowed : 25.33 % Favored : 71.45 % 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: -2.55 (0.30), residues: 765 helix: 0.06 (0.30), residues: 310 sheet: -1.89 (0.73), residues: 37 loop : -3.25 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 220 HIS 0.004 0.001 HIS A 582 PHE 0.024 0.001 PHE A 708 TYR 0.015 0.002 TYR A 605 ARG 0.007 0.001 ARG A 74 *********************** 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 to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7649 (tpp) cc_final: 0.7423 (tpp) REVERT: A 92 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7414 (mtm110) REVERT: A 119 LYS cc_start: 0.8759 (tppp) cc_final: 0.8366 (tppp) REVERT: A 148 MET cc_start: 0.6691 (tmm) cc_final: 0.6329 (tmm) REVERT: A 208 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7379 (mm-30) REVERT: A 223 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8464 (mtmm) REVERT: A 226 PHE cc_start: 0.8695 (t80) cc_final: 0.8330 (t80) REVERT: A 262 GLU cc_start: 0.7537 (pm20) cc_final: 0.7331 (pm20) REVERT: A 282 MET cc_start: 0.7172 (tpt) cc_final: 0.6773 (tpt) REVERT: A 332 MET cc_start: 0.5485 (pmm) cc_final: 0.4963 (pmm) REVERT: A 408 ARG cc_start: 0.8071 (tmm-80) cc_final: 0.7691 (tmm-80) REVERT: A 409 ASP cc_start: 0.7851 (t0) cc_final: 0.7500 (t0) REVERT: A 441 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8151 (mm) REVERT: A 443 LYS cc_start: 0.8476 (mtmm) cc_final: 0.8168 (mtmm) REVERT: A 455 ILE cc_start: 0.8534 (mm) cc_final: 0.8179 (tp) REVERT: A 457 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 532 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7621 (mm-30) REVERT: A 551 ASP cc_start: 0.7457 (t70) cc_final: 0.6940 (t0) REVERT: A 565 THR cc_start: 0.8332 (m) cc_final: 0.7890 (p) REVERT: A 570 ASN cc_start: 0.7600 (t160) cc_final: 0.7307 (t0) REVERT: A 585 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8419 (mmm-85) REVERT: A 598 GLU cc_start: 0.7594 (tt0) cc_final: 0.7310 (tt0) REVERT: A 624 LYS cc_start: 0.8056 (tptm) cc_final: 0.7674 (tttm) REVERT: A 630 ILE cc_start: 0.8629 (tp) cc_final: 0.8335 (tp) REVERT: A 674 TYR cc_start: 0.8384 (t80) cc_final: 0.8170 (t80) REVERT: A 695 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 723 LYS cc_start: 0.8143 (tmtt) cc_final: 0.7659 (tmtt) REVERT: A 766 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 808 VAL cc_start: 0.8797 (p) cc_final: 0.8437 (t) REVERT: A 812 LEU cc_start: 0.8609 (mt) cc_final: 0.8392 (mt) REVERT: A 814 GLN cc_start: 0.8146 (pp30) cc_final: 0.7742 (pp30) REVERT: A 865 LEU cc_start: 0.8690 (mm) cc_final: 0.8353 (mt) REVERT: A 867 LEU cc_start: 0.9057 (pp) cc_final: 0.8619 (pp) REVERT: A 871 PHE cc_start: 0.7758 (m-80) cc_final: 0.7441 (m-80) REVERT: A 873 TYR cc_start: 0.7441 (t80) cc_final: 0.7043 (t80) outliers start: 22 outliers final: 16 residues processed: 213 average time/residue: 0.2130 time to fit residues: 57.1511 Evaluate side-chains 219 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 725 THR Chi-restraints excluded: chain A residue 729 MET 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 52 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 35 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.158976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.141738 restraints weight = 10383.624| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.61 r_work: 0.3761 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6357 Z= 0.203 Angle : 0.752 14.081 8593 Z= 0.381 Chirality : 0.048 0.408 947 Planarity : 0.005 0.054 1089 Dihedral : 6.859 70.693 871 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.03 % Favored : 84.84 % Rotamer: Outliers : 2.64 % Allowed : 26.21 % Favored : 71.16 % 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: -2.51 (0.30), residues: 765 helix: 0.13 (0.30), residues: 309 sheet: -1.92 (0.72), residues: 37 loop : -3.25 (0.29), residues: 419 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 0.017 0.002 TYR A 605 ARG 0.006 0.001 ARG A 574 ********************** 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 218 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7648 (tpp) cc_final: 0.7429 (tpp) REVERT: A 92 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7450 (mtm110) REVERT: A 119 LYS cc_start: 0.8777 (tppp) cc_final: 0.8373 (tppp) REVERT: A 148 MET cc_start: 0.6707 (tmm) cc_final: 0.6343 (tmm) REVERT: A 158 GLU cc_start: 0.7599 (tp30) cc_final: 0.7336 (tp30) REVERT: A 180 VAL cc_start: 0.8681 (t) cc_final: 0.8458 (p) REVERT: A 208 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7384 (mm-30) REVERT: A 223 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8495 (mtmm) REVERT: A 226 PHE cc_start: 0.8711 (t80) cc_final: 0.8292 (t80) REVERT: A 262 GLU cc_start: 0.7523 (pm20) cc_final: 0.7305 (pm20) REVERT: A 282 MET cc_start: 0.7243 (tpt) cc_final: 0.6819 (tpt) REVERT: A 332 MET cc_start: 0.5493 (pmm) cc_final: 0.4968 (pmm) REVERT: A 408 ARG cc_start: 0.8087 (tmm-80) cc_final: 0.7711 (tmm-80) REVERT: A 441 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8146 (mm) REVERT: A 443 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8180 (mtmm) REVERT: A 455 ILE cc_start: 0.8506 (mm) cc_final: 0.8160 (tp) REVERT: A 457 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 532 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 551 ASP cc_start: 0.7491 (t70) cc_final: 0.7032 (t0) REVERT: A 565 THR cc_start: 0.8347 (m) cc_final: 0.7896 (p) REVERT: A 585 ARG cc_start: 0.8812 (mmm-85) cc_final: 0.8442 (mmm-85) REVERT: A 598 GLU cc_start: 0.7567 (tt0) cc_final: 0.7295 (tt0) REVERT: A 624 LYS cc_start: 0.7975 (tptm) cc_final: 0.7586 (tttm) REVERT: A 630 ILE cc_start: 0.8613 (tp) cc_final: 0.8350 (tp) REVERT: A 674 TYR cc_start: 0.8410 (t80) cc_final: 0.8191 (t80) REVERT: A 695 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 723 LYS cc_start: 0.8174 (tmtt) cc_final: 0.7677 (tmtt) REVERT: A 766 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8198 (tm-30) REVERT: A 808 VAL cc_start: 0.8804 (p) cc_final: 0.8444 (t) REVERT: A 812 LEU cc_start: 0.8643 (mt) cc_final: 0.8386 (mt) REVERT: A 814 GLN cc_start: 0.8200 (pp30) cc_final: 0.7762 (pp30) REVERT: A 865 LEU cc_start: 0.8689 (mm) cc_final: 0.8387 (mt) REVERT: A 867 LEU cc_start: 0.9075 (pp) cc_final: 0.8640 (pp) REVERT: A 871 PHE cc_start: 0.7765 (m-80) cc_final: 0.7432 (m-80) REVERT: A 873 TYR cc_start: 0.7451 (t80) cc_final: 0.7042 (t80) outliers start: 18 outliers final: 15 residues processed: 209 average time/residue: 0.2121 time to fit residues: 55.9395 Evaluate side-chains 214 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 76 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.156423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.139183 restraints weight = 10452.688| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.59 r_work: 0.3726 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6357 Z= 0.262 Angle : 0.773 14.265 8593 Z= 0.396 Chirality : 0.049 0.416 947 Planarity : 0.005 0.058 1089 Dihedral : 6.986 66.794 871 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.82 % Favored : 84.05 % Rotamer: Outliers : 2.49 % Allowed : 26.35 % Favored : 71.16 % 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: -2.53 (0.30), residues: 765 helix: 0.12 (0.30), residues: 308 sheet: -1.95 (0.73), residues: 37 loop : -3.26 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS A 582 PHE 0.027 0.002 PHE A 888 TYR 0.020 0.002 TYR A 605 ARG 0.006 0.001 ARG A 574 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3285.18 seconds wall clock time: 57 minutes 12.42 seconds (3432.42 seconds total)