Starting phenix.real_space_refine on Tue Sep 24 00:58:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/09_2024/6vrl_21370.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/09_2024/6vrl_21370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/09_2024/6vrl_21370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/09_2024/6vrl_21370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/09_2024/6vrl_21370.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/09_2024/6vrl_21370.cif" } resolution = 3.8 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= 0.971 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 92 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 I 1 10.91 5 S 34 5.16 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'LMT': 1, 'NAG': 2, 'RFY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.96, per 1000 atoms: 0.81 Number of scatterers: 6141 At special positions: 0 Unit cell: (95.256, 104.328, 82.296, 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) I 1 52.95 S 34 16.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 208 " " NAG A 702 " - " ASN A 217 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 866.8 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 53.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.540A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 128 through 144 removed outlier: 4.110A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.256A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 253 through 271 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.721A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.665A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 removed outlier: 4.080A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 322 through 338 removed outlier: 4.094A pdb=" N TRP A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 356 through 390 removed outlier: 3.531A pdb=" N ASP A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 419 through 454 removed outlier: 4.039A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.832A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 543 Processing helix chain 'A' and resid 543 through 557 Processing helix chain 'A' and resid 571 through 587 removed outlier: 4.254A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'B' and resid 81 through 84 removed outlier: 4.011A pdb=" N LYS B 84 " --> pdb=" O GLN B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 84' Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565 removed outlier: 3.666A pdb=" N LEU A 565 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.797A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.811A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 102 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.649A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASN B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N MET B 53 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 112 " --> pdb=" O GLN B 58 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 888 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: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 2681 1.40 - 1.58: 3595 1.58 - 1.75: 0 1.75 - 1.93: 49 1.93 - 2.11: 1 Bond restraints: 6326 Sorted by residual: bond pdb=" C06 RFY A 704 " pdb=" C07 RFY A 704 " ideal model delta sigma weight residual 1.511 1.576 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C05 RFY A 704 " pdb=" C06 RFY A 704 " ideal model delta sigma weight residual 1.543 1.493 0.050 2.00e-02 2.50e+03 6.30e+00 bond pdb=" C17 RFY A 704 " pdb=" C18 RFY A 704 " ideal model delta sigma weight residual 1.370 1.418 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C19 RFY A 704 " pdb=" C20 RFY A 704 " ideal model delta sigma weight residual 1.371 1.416 -0.045 2.00e-02 2.50e+03 5.11e+00 bond pdb=" C01 RFY A 704 " pdb=" C06 RFY A 704 " ideal model delta sigma weight residual 1.542 1.498 0.044 2.00e-02 2.50e+03 4.95e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 8430 1.79 - 3.57: 150 3.57 - 5.36: 25 5.36 - 7.15: 10 7.15 - 8.94: 4 Bond angle restraints: 8619 Sorted by residual: angle pdb=" N VAL A 397 " pdb=" CA VAL A 397 " pdb=" C VAL A 397 " ideal model delta sigma weight residual 113.42 109.33 4.09 1.17e+00 7.31e-01 1.22e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.12 -7.31 2.21e+00 2.05e-01 1.09e+01 angle pdb=" C2 LMT A 703 " pdb=" C3 LMT A 703 " pdb=" C4 LMT A 703 " ideal model delta sigma weight residual 117.09 108.15 8.94 3.00e+00 1.11e-01 8.87e+00 angle pdb=" C10 LMT A 703 " pdb=" C9 LMT A 703 " pdb=" C8 LMT A 703 " ideal model delta sigma weight residual 116.03 107.32 8.71 3.00e+00 1.11e-01 8.43e+00 angle pdb=" C VAL B 120 " pdb=" N ARG B 121 " pdb=" CA ARG B 121 " ideal model delta sigma weight residual 121.80 128.79 -6.99 2.44e+00 1.68e-01 8.20e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3299 17.53 - 35.07: 321 35.07 - 52.60: 54 52.60 - 70.14: 14 70.14 - 87.67: 4 Dihedral angle restraints: 3692 sinusoidal: 1478 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 128.14 51.86 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual 93.00 133.61 -40.61 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" CA CYS A 209 " pdb=" C CYS A 209 " pdb=" N THR A 210 " pdb=" CA THR A 210 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 714 0.042 - 0.083: 207 0.083 - 0.125: 40 0.125 - 0.166: 1 0.166 - 0.208: 4 Chirality restraints: 966 Sorted by residual: chirality pdb=" C4' LMT A 703 " pdb=" C3' LMT A 703 " pdb=" C5' LMT A 703 " pdb=" O1B LMT A 703 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C3B LMT A 703 " pdb=" C2B LMT A 703 " pdb=" C4B LMT A 703 " pdb=" O3B LMT A 703 " both_signs ideal model delta sigma weight residual False 2.50 2.29 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C5' LMT A 703 " pdb=" C4' LMT A 703 " pdb=" C6' LMT A 703 " pdb=" O5' LMT A 703 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO B 122 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 465 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C PHE A 465 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE A 465 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 466 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 590 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " 0.017 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.72: 256 2.72 - 3.28: 6880 3.28 - 3.84: 11030 3.84 - 4.40: 13024 4.40 - 4.96: 22133 Nonbonded interactions: 53323 Sorted by model distance: nonbonded pdb=" OG1 THR C 83 " pdb=" O THR C 94 " model vdw 2.159 3.040 nonbonded pdb=" OG SER B 110 " pdb=" O LEU B 134 " model vdw 2.173 3.040 nonbonded pdb=" O THR A 221 " pdb=" OG SER A 224 " model vdw 2.202 3.040 nonbonded pdb=" O ASP C 102 " pdb=" OH TYR C 106 " model vdw 2.235 3.040 nonbonded pdb=" O SER A 559 " pdb=" O6' LMT A 703 " model vdw 2.267 3.040 ... (remaining 53318 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.380 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 0.065 6326 Z= 0.237 Angle : 0.633 8.936 8619 Z= 0.327 Chirality : 0.040 0.208 966 Planarity : 0.004 0.067 1048 Dihedral : 13.973 87.674 2277 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -3.12 (0.27), residues: 758 helix: -0.96 (0.24), residues: 360 sheet: -3.12 (0.42), residues: 99 loop : -3.02 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 151 HIS 0.001 0.000 HIS A 143 PHE 0.015 0.001 PHE A 311 TYR 0.013 0.001 TYR B 123 ARG 0.001 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TRP cc_start: 0.8013 (m100) cc_final: 0.7795 (m100) REVERT: A 134 TYR cc_start: 0.7065 (t80) cc_final: 0.6847 (t80) REVERT: A 135 MET cc_start: 0.7156 (ttm) cc_final: 0.6385 (ttm) REVERT: A 136 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6434 (mm-30) REVERT: A 151 TRP cc_start: 0.7689 (m100) cc_final: 0.7139 (m100) REVERT: A 179 ILE cc_start: 0.8987 (mm) cc_final: 0.8532 (mt) REVERT: A 234 ARG cc_start: 0.6268 (ttm-80) cc_final: 0.5843 (mtt-85) REVERT: A 373 PHE cc_start: 0.8209 (t80) cc_final: 0.7918 (t80) REVERT: A 408 ILE cc_start: 0.8773 (mt) cc_final: 0.8554 (mt) REVERT: A 494 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6481 (mm-30) REVERT: A 553 ILE cc_start: 0.9053 (pt) cc_final: 0.8831 (pt) REVERT: C 47 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7393 (tm-30) REVERT: C 67 LEU cc_start: 0.6982 (mm) cc_final: 0.6741 (mm) REVERT: C 114 ILE cc_start: 0.8801 (pt) cc_final: 0.8581 (mp) REVERT: B 42 LYS cc_start: 0.6139 (mttt) cc_final: 0.5449 (tptt) REVERT: B 53 MET cc_start: 0.8867 (tpp) cc_final: 0.8515 (tpt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1616 time to fit residues: 44.2370 Evaluate side-chains 148 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.0050 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.172 Angle : 0.622 10.165 8619 Z= 0.311 Chirality : 0.041 0.245 966 Planarity : 0.004 0.072 1048 Dihedral : 7.263 77.856 961 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.46 % Allowed : 15.23 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.30), residues: 758 helix: 0.26 (0.26), residues: 363 sheet: -2.56 (0.46), residues: 100 loop : -2.44 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 220 HIS 0.004 0.001 HIS C 111 PHE 0.018 0.001 PHE A 423 TYR 0.019 0.001 TYR B 123 ARG 0.005 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6560 (mm-30) REVERT: A 151 TRP cc_start: 0.7719 (m100) cc_final: 0.7057 (m100) REVERT: A 240 HIS cc_start: 0.7108 (p90) cc_final: 0.6633 (m170) REVERT: A 373 PHE cc_start: 0.8238 (t80) cc_final: 0.7746 (t80) REVERT: A 388 GLU cc_start: 0.6680 (tm-30) cc_final: 0.6401 (tm-30) REVERT: A 410 TYR cc_start: 0.8338 (t80) cc_final: 0.8086 (t80) REVERT: A 417 MET cc_start: 0.6346 (mtm) cc_final: 0.5887 (mtm) REVERT: A 494 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6516 (mm-30) REVERT: A 553 ILE cc_start: 0.9102 (pt) cc_final: 0.8895 (pt) REVERT: C 101 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6923 (tp30) REVERT: B 42 LYS cc_start: 0.6307 (mttt) cc_final: 0.5758 (tptt) REVERT: B 53 MET cc_start: 0.9059 (tpp) cc_final: 0.8778 (tpt) outliers start: 16 outliers final: 8 residues processed: 170 average time/residue: 0.1565 time to fit residues: 35.8756 Evaluate side-chains 150 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.0670 chunk 73 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.169 Angle : 0.612 11.573 8619 Z= 0.304 Chirality : 0.041 0.223 966 Planarity : 0.004 0.072 1048 Dihedral : 7.045 76.609 961 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.00 % Allowed : 20.31 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.31), residues: 758 helix: 0.82 (0.27), residues: 353 sheet: -2.41 (0.46), residues: 100 loop : -2.02 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 103 HIS 0.004 0.001 HIS C 111 PHE 0.019 0.001 PHE A 423 TYR 0.018 0.001 TYR B 123 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6806 (mm-30) REVERT: A 151 TRP cc_start: 0.7791 (m100) cc_final: 0.7156 (m100) REVERT: A 410 TYR cc_start: 0.8335 (t80) cc_final: 0.7972 (t80) REVERT: A 494 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6433 (mm-30) REVERT: A 553 ILE cc_start: 0.9123 (pt) cc_final: 0.8877 (pt) REVERT: C 101 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6991 (tp30) REVERT: B 42 LYS cc_start: 0.6247 (mttt) cc_final: 0.5744 (tptt) REVERT: B 126 ASP cc_start: 0.8074 (m-30) cc_final: 0.7247 (p0) outliers start: 13 outliers final: 10 residues processed: 154 average time/residue: 0.1591 time to fit residues: 33.5536 Evaluate side-chains 148 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.0470 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 0.0370 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.161 Angle : 0.596 9.657 8619 Z= 0.297 Chirality : 0.040 0.189 966 Planarity : 0.004 0.071 1048 Dihedral : 6.776 76.230 961 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.92 % Allowed : 21.38 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.30), residues: 758 helix: 0.85 (0.27), residues: 355 sheet: -2.22 (0.46), residues: 100 loop : -1.91 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 55 HIS 0.004 0.001 HIS C 111 PHE 0.022 0.001 PHE A 521 TYR 0.026 0.001 TYR A 134 ARG 0.005 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6953 (mm-30) REVERT: A 151 TRP cc_start: 0.7779 (m100) cc_final: 0.7115 (m100) REVERT: A 410 TYR cc_start: 0.8310 (t80) cc_final: 0.7962 (t80) REVERT: A 417 MET cc_start: 0.6434 (mtm) cc_final: 0.5867 (mtm) REVERT: A 494 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6379 (mm-30) REVERT: A 553 ILE cc_start: 0.9151 (pt) cc_final: 0.8908 (pt) REVERT: B 64 LEU cc_start: 0.8654 (mm) cc_final: 0.8424 (mm) outliers start: 19 outliers final: 14 residues processed: 147 average time/residue: 0.1480 time to fit residues: 29.9694 Evaluate side-chains 143 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 0.1980 chunk 65 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6326 Z= 0.165 Angle : 0.605 10.011 8619 Z= 0.301 Chirality : 0.041 0.252 966 Planarity : 0.004 0.070 1048 Dihedral : 6.592 75.553 961 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.46 % Allowed : 23.38 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.31), residues: 758 helix: 0.85 (0.27), residues: 356 sheet: -2.06 (0.46), residues: 100 loop : -1.74 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 103 HIS 0.004 0.001 HIS C 111 PHE 0.023 0.001 PHE A 521 TYR 0.023 0.001 TYR A 134 ARG 0.003 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 151 TRP cc_start: 0.7771 (m100) cc_final: 0.7084 (m100) REVERT: A 410 TYR cc_start: 0.8275 (t80) cc_final: 0.7953 (t80) REVERT: A 417 MET cc_start: 0.6332 (mtm) cc_final: 0.5957 (mtm) REVERT: A 494 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6447 (mm-30) REVERT: A 553 ILE cc_start: 0.9149 (pt) cc_final: 0.8896 (pt) REVERT: C 101 GLU cc_start: 0.7198 (tp30) cc_final: 0.6871 (tp30) outliers start: 16 outliers final: 14 residues processed: 146 average time/residue: 0.1478 time to fit residues: 29.9215 Evaluate side-chains 148 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6326 Z= 0.182 Angle : 0.628 12.489 8619 Z= 0.315 Chirality : 0.042 0.303 966 Planarity : 0.004 0.072 1048 Dihedral : 6.640 72.755 961 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.92 % Allowed : 23.38 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.31), residues: 758 helix: 0.92 (0.27), residues: 356 sheet: -1.92 (0.49), residues: 96 loop : -1.67 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 55 HIS 0.005 0.001 HIS C 111 PHE 0.019 0.001 PHE A 428 TYR 0.023 0.002 TYR A 134 ARG 0.003 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6965 (mm-30) REVERT: A 151 TRP cc_start: 0.7877 (m100) cc_final: 0.7296 (m100) REVERT: A 410 TYR cc_start: 0.8303 (t80) cc_final: 0.7993 (t80) REVERT: A 417 MET cc_start: 0.6351 (mtm) cc_final: 0.6045 (mtm) REVERT: A 494 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6486 (mm-30) REVERT: A 553 ILE cc_start: 0.9173 (pt) cc_final: 0.8922 (pt) REVERT: C 31 MET cc_start: 0.6438 (ppp) cc_final: 0.6168 (tmm) REVERT: C 101 GLU cc_start: 0.7344 (tp30) cc_final: 0.6989 (tp30) REVERT: B 58 GLN cc_start: 0.4970 (OUTLIER) cc_final: 0.4407 (tp40) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.1560 time to fit residues: 31.7910 Evaluate side-chains 150 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6326 Z= 0.212 Angle : 0.642 9.606 8619 Z= 0.326 Chirality : 0.043 0.294 966 Planarity : 0.004 0.073 1048 Dihedral : 6.699 74.187 961 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.92 % Allowed : 24.31 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.31), residues: 758 helix: 0.86 (0.27), residues: 356 sheet: -1.98 (0.48), residues: 96 loop : -1.63 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 55 HIS 0.004 0.001 HIS C 111 PHE 0.026 0.001 PHE A 311 TYR 0.022 0.002 TYR B 123 ARG 0.003 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7019 (mm-30) REVERT: A 410 TYR cc_start: 0.8275 (t80) cc_final: 0.8053 (t80) REVERT: A 492 LEU cc_start: 0.8384 (mt) cc_final: 0.8121 (mt) REVERT: A 494 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6525 (mm-30) REVERT: A 553 ILE cc_start: 0.9174 (pt) cc_final: 0.8917 (pt) REVERT: C 74 ARG cc_start: 0.6920 (ptt-90) cc_final: 0.6664 (ptp90) REVERT: C 101 GLU cc_start: 0.7402 (tp30) cc_final: 0.7105 (tp30) REVERT: B 58 GLN cc_start: 0.4926 (OUTLIER) cc_final: 0.4313 (tp40) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.1804 time to fit residues: 36.4687 Evaluate side-chains 149 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6326 Z= 0.207 Angle : 0.653 10.223 8619 Z= 0.328 Chirality : 0.042 0.269 966 Planarity : 0.004 0.074 1048 Dihedral : 6.749 74.774 961 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.08 % Allowed : 25.54 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.31), residues: 758 helix: 0.83 (0.27), residues: 355 sheet: -2.01 (0.47), residues: 96 loop : -1.60 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 103 HIS 0.003 0.001 HIS C 111 PHE 0.019 0.001 PHE A 428 TYR 0.024 0.002 TYR B 123 ARG 0.005 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6996 (mm-30) REVERT: A 180 MET cc_start: 0.8157 (mmp) cc_final: 0.7660 (mmm) REVERT: A 410 TYR cc_start: 0.8220 (t80) cc_final: 0.7982 (t80) REVERT: A 492 LEU cc_start: 0.8392 (mt) cc_final: 0.8133 (mt) REVERT: A 494 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6529 (mm-30) REVERT: A 553 ILE cc_start: 0.9196 (pt) cc_final: 0.8927 (pt) REVERT: C 74 ARG cc_start: 0.6962 (ptt-90) cc_final: 0.6655 (ptp90) REVERT: C 101 GLU cc_start: 0.7430 (tp30) cc_final: 0.7060 (tp30) REVERT: B 58 GLN cc_start: 0.4945 (OUTLIER) cc_final: 0.4322 (tp40) outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 0.1527 time to fit residues: 31.9045 Evaluate side-chains 153 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6326 Z= 0.201 Angle : 0.656 10.110 8619 Z= 0.329 Chirality : 0.042 0.256 966 Planarity : 0.004 0.074 1048 Dihedral : 6.799 75.033 961 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.23 % Allowed : 25.69 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.31), residues: 758 helix: 0.88 (0.27), residues: 355 sheet: -1.92 (0.47), residues: 95 loop : -1.60 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 103 HIS 0.003 0.001 HIS C 111 PHE 0.022 0.001 PHE A 311 TYR 0.024 0.002 TYR B 123 ARG 0.005 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7016 (mm-30) REVERT: A 180 MET cc_start: 0.8159 (mmp) cc_final: 0.7714 (mmm) REVERT: A 410 TYR cc_start: 0.8158 (t80) cc_final: 0.7922 (t80) REVERT: A 494 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6550 (mm-30) REVERT: A 553 ILE cc_start: 0.9203 (pt) cc_final: 0.8934 (pt) REVERT: C 74 ARG cc_start: 0.6900 (ptt-90) cc_final: 0.6581 (ptp90) REVERT: B 58 GLN cc_start: 0.4935 (OUTLIER) cc_final: 0.4312 (tp40) outliers start: 21 outliers final: 18 residues processed: 150 average time/residue: 0.1468 time to fit residues: 30.4375 Evaluate side-chains 153 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 0.0010 chunk 59 optimal weight: 0.0040 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.168 Angle : 0.645 10.411 8619 Z= 0.323 Chirality : 0.042 0.256 966 Planarity : 0.004 0.073 1048 Dihedral : 6.701 74.001 961 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.62 % Allowed : 26.31 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.31), residues: 758 helix: 0.99 (0.28), residues: 354 sheet: -1.68 (0.47), residues: 99 loop : -1.59 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 103 HIS 0.003 0.001 HIS C 111 PHE 0.023 0.001 PHE A 311 TYR 0.023 0.001 TYR B 123 ARG 0.004 0.000 ARG C 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6926 (mm-30) REVERT: A 151 TRP cc_start: 0.7811 (m100) cc_final: 0.7170 (m100) REVERT: A 180 MET cc_start: 0.8112 (mmp) cc_final: 0.7597 (mmm) REVERT: A 370 MET cc_start: 0.5965 (mtt) cc_final: 0.5554 (mtt) REVERT: A 410 TYR cc_start: 0.8103 (t80) cc_final: 0.7812 (t80) REVERT: A 475 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: A 494 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6466 (mm-30) REVERT: A 553 ILE cc_start: 0.9166 (pt) cc_final: 0.8903 (pt) REVERT: C 74 ARG cc_start: 0.6729 (ptt-90) cc_final: 0.6443 (ptp90) REVERT: B 58 GLN cc_start: 0.4876 (OUTLIER) cc_final: 0.4282 (tp40) outliers start: 17 outliers final: 14 residues processed: 153 average time/residue: 0.1773 time to fit residues: 37.1586 Evaluate side-chains 147 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.191360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.174513 restraints weight = 10508.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.178681 restraints weight = 6495.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.181512 restraints weight = 4294.939| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6326 Z= 0.166 Angle : 0.658 10.449 8619 Z= 0.324 Chirality : 0.041 0.245 966 Planarity : 0.004 0.073 1048 Dihedral : 6.465 72.321 961 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.31 % Allowed : 26.77 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.31), residues: 758 helix: 0.99 (0.27), residues: 355 sheet: -1.50 (0.49), residues: 94 loop : -1.57 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 55 HIS 0.003 0.001 HIS C 111 PHE 0.023 0.001 PHE A 311 TYR 0.020 0.001 TYR B 123 ARG 0.003 0.000 ARG C 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.27 seconds wall clock time: 33 minutes 7.63 seconds (1987.63 seconds total)