Starting phenix.real_space_refine on Sun Mar 10 23:58:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/03_2024/7li8_23363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/03_2024/7li8_23363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/03_2024/7li8_23363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/03_2024/7li8_23363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/03_2024/7li8_23363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/03_2024/7li8_23363_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4104 2.51 5 N 962 2.21 5 O 1081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6181 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4303 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 515} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Unusual residues: {'D10': 1, 'D12': 3, 'HP6': 6, 'LNK': 1, 'R16': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 4.09, per 1000 atoms: 0.66 Number of scatterers: 6181 At special positions: 0 Unit cell: (68.688, 77.112, 122.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1081 8.00 N 962 7.00 C 4104 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 B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.3 seconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 4 sheets defined 43.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 99 through 102 No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.803A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.628A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 4.556A pdb=" N PHE A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 4.317A pdb=" N SER A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.344A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 360 through 388 removed outlier: 3.988A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 403 through 416 removed outlier: 3.750A pdb=" N LEU A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 408 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 416 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 removed outlier: 4.117A pdb=" N ALA A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 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 486 through 492 removed outlier: 4.382A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.729A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Proline residue: A 546 - end of helix Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.732A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing sheet with id= A, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.633A pdb=" N GLN B 24 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 42 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.605A pdb=" N ILE B 70 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 68 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP B 66 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG B 59 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 64 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 109 through 114 removed outlier: 3.730A pdb=" N PHE C 111 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE C 60 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN C 61 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU C 70 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 87 through 90 removed outlier: 3.561A pdb=" N SER C 89 " --> pdb=" O SER C 96 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 591 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: 1.60 Time building geometry restraints manager: 2.55 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: 1811 1.34 - 1.46: 1452 1.46 - 1.58: 3037 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6349 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.50e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 6344 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.49: 231 107.49 - 114.11: 3541 114.11 - 120.74: 2686 120.74 - 127.36: 2056 127.36 - 133.99: 82 Bond angle restraints: 8596 Sorted by residual: angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 113.53 109.27 4.26 9.80e-01 1.04e+00 1.89e+01 angle pdb=" N VAL A 92 " pdb=" CA VAL A 92 " pdb=" C VAL A 92 " ideal model delta sigma weight residual 113.71 110.54 3.17 9.50e-01 1.11e+00 1.11e+01 angle pdb=" N VAL A 446 " pdb=" CA VAL A 446 " pdb=" C VAL A 446 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.07e+01 angle pdb=" C GLY B 121 " pdb=" N SER B 122 " pdb=" CA SER B 122 " ideal model delta sigma weight residual 120.38 124.54 -4.16 1.37e+00 5.33e-01 9.22e+00 angle pdb=" C MET B 127 " pdb=" N ASP B 128 " pdb=" CA ASP B 128 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 ... (remaining 8591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 3326 14.73 - 29.46: 272 29.46 - 44.19: 59 44.19 - 58.91: 9 58.91 - 73.64: 2 Dihedral angle restraints: 3668 sinusoidal: 1462 harmonic: 2206 Sorted by residual: dihedral pdb=" CB CYS B 41 " pdb=" SG CYS B 41 " pdb=" SG CYS B 115 " pdb=" CB CYS B 115 " ideal model delta sinusoidal sigma weight residual 93.00 166.64 -73.64 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CA TRP A 204 " pdb=" C TRP A 204 " pdb=" N ASN A 205 " pdb=" CA ASN A 205 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP A 87 " pdb=" CB ASP A 87 " pdb=" CG ASP A 87 " pdb=" OD1 ASP A 87 " ideal model delta sinusoidal sigma weight residual -30.00 -82.66 52.66 1 2.00e+01 2.50e-03 9.44e+00 ... (remaining 3665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 929 0.103 - 0.206: 12 0.206 - 0.309: 0 0.309 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 942 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.65e+02 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB THR C 107 " pdb=" CA THR C 107 " pdb=" OG1 THR C 107 " pdb=" CG2 THR C 107 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 939 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 338 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 339 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 131 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 128 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ASP B 128 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP B 128 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR B 129 " -0.006 2.00e-02 2.50e+03 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1069 2.76 - 3.30: 5783 3.30 - 3.83: 9983 3.83 - 4.37: 10915 4.37 - 4.90: 19159 Nonbonded interactions: 46909 Sorted by model distance: nonbonded pdb=" OH TYR A 110 " pdb=" O VAL A 394 " model vdw 2.230 2.440 nonbonded pdb=" OG SER B 49 " pdb=" O PRO B 72 " model vdw 2.256 2.440 nonbonded pdb=" O LYS A 201 " pdb=" NE1 TRP B 52 " model vdw 2.296 2.520 nonbonded pdb=" O SER A 477 " pdb=" OG SER A 477 " model vdw 2.303 2.440 nonbonded pdb=" OG SER B 36 " pdb=" O LEU B 102 " model vdw 2.330 2.440 ... (remaining 46904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 13.460 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.760 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.002 0.031 6349 Z= 0.127 Angle : 0.601 5.403 8596 Z= 0.300 Chirality : 0.041 0.516 942 Planarity : 0.003 0.033 1047 Dihedral : 10.905 69.682 2259 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: -3.23 (0.27), residues: 761 helix: -1.23 (0.23), residues: 353 sheet: -2.94 (0.51), residues: 82 loop : -2.92 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.000 TRP A 204 HIS 0.001 0.000 HIS A 223 PHE 0.013 0.000 PHE B 125 TYR 0.011 0.001 TYR A 175 ARG 0.001 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6008 (mmpt) cc_final: 0.5241 (ptmt) REVERT: A 152 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8428 (mmt90) REVERT: A 222 LEU cc_start: 0.7905 (tp) cc_final: 0.7315 (tp) REVERT: B 58 GLN cc_start: 0.8476 (tt0) cc_final: 0.8096 (tt0) REVERT: C 62 GLN cc_start: 0.8044 (tt0) cc_final: 0.7838 (tt0) REVERT: C 110 TYR cc_start: 0.7845 (m-80) cc_final: 0.7568 (m-80) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2189 time to fit residues: 42.3450 Evaluate side-chains 117 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.0970 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 194 GLN A 354 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6349 Z= 0.160 Angle : 0.546 9.430 8596 Z= 0.267 Chirality : 0.040 0.246 942 Planarity : 0.004 0.030 1047 Dihedral : 4.528 57.862 946 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.64 % Allowed : 12.44 % Favored : 84.91 % 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: -2.14 (0.30), residues: 761 helix: -0.32 (0.26), residues: 350 sheet: -2.39 (0.52), residues: 86 loop : -2.35 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 59 HIS 0.003 0.001 HIS C 100 PHE 0.025 0.001 PHE A 287 TYR 0.026 0.001 TYR A 358 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6016 (mmpt) cc_final: 0.5213 (ptmt) REVERT: A 222 LEU cc_start: 0.7928 (tp) cc_final: 0.7708 (tp) REVERT: A 260 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7284 (tmm) REVERT: A 592 TYR cc_start: 0.8618 (t80) cc_final: 0.8322 (t80) REVERT: C 44 ARG cc_start: 0.7242 (mmm160) cc_final: 0.6792 (mmm160) REVERT: C 110 TYR cc_start: 0.7943 (m-80) cc_final: 0.7650 (m-80) outliers start: 17 outliers final: 14 residues processed: 137 average time/residue: 0.1886 time to fit residues: 33.7349 Evaluate side-chains 120 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 0.0170 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6349 Z= 0.154 Angle : 0.528 9.416 8596 Z= 0.256 Chirality : 0.039 0.242 942 Planarity : 0.004 0.030 1047 Dihedral : 4.424 57.527 946 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.73 % Allowed : 13.84 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.31), residues: 761 helix: 0.04 (0.28), residues: 349 sheet: -2.06 (0.54), residues: 86 loop : -2.17 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 535 HIS 0.002 0.001 HIS C 100 PHE 0.023 0.001 PHE A 548 TYR 0.016 0.001 TYR B 120 ARG 0.006 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6044 (mmpt) cc_final: 0.5196 (ptmt) REVERT: A 260 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7115 (tmm) REVERT: A 328 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7499 (t0) REVERT: A 592 TYR cc_start: 0.8606 (t80) cc_final: 0.8394 (t80) REVERT: C 102 MET cc_start: 0.7585 (tmm) cc_final: 0.7312 (tmm) REVERT: C 110 TYR cc_start: 0.8015 (m-80) cc_final: 0.7742 (m-80) REVERT: C 116 LYS cc_start: 0.5487 (mttp) cc_final: 0.3679 (ttmt) outliers start: 24 outliers final: 16 residues processed: 129 average time/residue: 0.1782 time to fit residues: 30.4765 Evaluate side-chains 124 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 19 optimal weight: 0.0020 chunk 60 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6349 Z= 0.160 Angle : 0.543 9.418 8596 Z= 0.263 Chirality : 0.040 0.242 942 Planarity : 0.004 0.030 1047 Dihedral : 4.477 57.874 946 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.20 % Allowed : 15.24 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.31), residues: 761 helix: 0.19 (0.28), residues: 351 sheet: -1.92 (0.52), residues: 97 loop : -2.07 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 535 HIS 0.002 0.001 HIS A 223 PHE 0.024 0.001 PHE A 586 TYR 0.029 0.001 TYR A 358 ARG 0.006 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6070 (mmpt) cc_final: 0.5199 (ptmt) REVERT: A 229 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8138 (tp30) REVERT: A 260 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7276 (tmm) REVERT: A 328 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7560 (t0) REVERT: A 385 TYR cc_start: 0.7284 (t80) cc_final: 0.6895 (t80) REVERT: A 548 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.5869 (t80) REVERT: A 567 GLN cc_start: 0.7711 (mp10) cc_final: 0.7291 (mp10) REVERT: B 53 MET cc_start: 0.7133 (ttt) cc_final: 0.6904 (ttm) REVERT: C 102 MET cc_start: 0.7524 (tmm) cc_final: 0.7208 (tmm) REVERT: C 110 TYR cc_start: 0.8050 (m-80) cc_final: 0.7792 (m-80) outliers start: 27 outliers final: 21 residues processed: 131 average time/residue: 0.1727 time to fit residues: 30.3598 Evaluate side-chains 131 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 0.0570 chunk 24 optimal weight: 0.0050 overall best weight: 1.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6349 Z= 0.232 Angle : 0.595 9.340 8596 Z= 0.293 Chirality : 0.041 0.237 942 Planarity : 0.004 0.053 1047 Dihedral : 4.814 57.256 946 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.35 % Allowed : 17.42 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.31), residues: 761 helix: 0.18 (0.28), residues: 355 sheet: -1.66 (0.54), residues: 98 loop : -1.97 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 204 HIS 0.004 0.001 HIS A 223 PHE 0.021 0.001 PHE A 377 TYR 0.030 0.002 TYR B 120 ARG 0.010 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6063 (mmpt) cc_final: 0.5180 (ptmt) REVERT: A 229 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 548 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6213 (t80) REVERT: A 567 GLN cc_start: 0.7742 (mp10) cc_final: 0.7353 (mp10) REVERT: B 53 MET cc_start: 0.7239 (ttt) cc_final: 0.6877 (ttm) REVERT: C 102 MET cc_start: 0.7502 (tmm) cc_final: 0.7125 (tmm) outliers start: 28 outliers final: 22 residues processed: 130 average time/residue: 0.1800 time to fit residues: 31.2410 Evaluate side-chains 129 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6349 Z= 0.191 Angle : 0.603 10.755 8596 Z= 0.288 Chirality : 0.041 0.234 942 Planarity : 0.004 0.032 1047 Dihedral : 4.803 57.365 946 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.67 % Allowed : 18.35 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.31), residues: 761 helix: 0.30 (0.28), residues: 353 sheet: -1.50 (0.55), residues: 97 loop : -1.98 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.003 0.001 HIS A 223 PHE 0.021 0.001 PHE A 377 TYR 0.030 0.002 TYR B 120 ARG 0.005 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6107 (mmpt) cc_final: 0.5233 (ptmt) REVERT: A 229 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8427 (tm-30) REVERT: A 260 MET cc_start: 0.7620 (tmm) cc_final: 0.7361 (tmt) REVERT: A 464 ARG cc_start: 0.7068 (mmp80) cc_final: 0.4516 (tpp-160) REVERT: A 548 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6378 (t80) REVERT: A 567 GLN cc_start: 0.7727 (mp10) cc_final: 0.7367 (mp10) REVERT: B 53 MET cc_start: 0.7236 (ttt) cc_final: 0.6860 (ttm) REVERT: C 38 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7450 (mmm-85) REVERT: C 102 MET cc_start: 0.7512 (tmm) cc_final: 0.7146 (tmm) outliers start: 30 outliers final: 25 residues processed: 137 average time/residue: 0.1744 time to fit residues: 31.8837 Evaluate side-chains 135 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6349 Z= 0.314 Angle : 0.696 10.426 8596 Z= 0.335 Chirality : 0.043 0.225 942 Planarity : 0.004 0.027 1047 Dihedral : 5.376 57.100 946 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 5.29 % Allowed : 19.44 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.31), residues: 761 helix: 0.22 (0.28), residues: 352 sheet: -1.54 (0.55), residues: 98 loop : -2.12 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 204 HIS 0.003 0.001 HIS A 223 PHE 0.024 0.002 PHE A 377 TYR 0.026 0.002 TYR B 120 ARG 0.008 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6091 (mmpt) cc_final: 0.5148 (ptmt) REVERT: A 260 MET cc_start: 0.7702 (tmm) cc_final: 0.7415 (tmt) REVERT: A 271 TRP cc_start: 0.7733 (OUTLIER) cc_final: 0.7271 (t60) REVERT: A 548 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6788 (t80) REVERT: C 38 ARG cc_start: 0.7835 (mtp-110) cc_final: 0.7569 (mmm-85) REVERT: C 102 MET cc_start: 0.7517 (tmm) cc_final: 0.7079 (tmm) REVERT: C 105 ASP cc_start: 0.8065 (t0) cc_final: 0.7831 (t0) outliers start: 34 outliers final: 26 residues processed: 140 average time/residue: 0.1689 time to fit residues: 31.5792 Evaluate side-chains 135 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6349 Z= 0.169 Angle : 0.651 10.670 8596 Z= 0.304 Chirality : 0.042 0.237 942 Planarity : 0.003 0.025 1047 Dihedral : 4.963 57.151 946 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.35 % Allowed : 20.22 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.31), residues: 761 helix: 0.40 (0.29), residues: 352 sheet: -1.39 (0.57), residues: 85 loop : -2.01 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 59 HIS 0.002 0.001 HIS A 223 PHE 0.024 0.001 PHE A 586 TYR 0.031 0.002 TYR A 358 ARG 0.005 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6150 (mmpt) cc_final: 0.5226 (ptmt) REVERT: A 260 MET cc_start: 0.7588 (tmm) cc_final: 0.7287 (tmt) REVERT: A 464 ARG cc_start: 0.7287 (mmp80) cc_final: 0.4748 (tpp80) REVERT: A 548 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6754 (t80) REVERT: A 567 GLN cc_start: 0.7779 (mp10) cc_final: 0.7408 (mp10) REVERT: B 47 ARG cc_start: 0.7448 (mtm180) cc_final: 0.7181 (mtm-85) REVERT: C 38 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7419 (mmm-85) REVERT: C 102 MET cc_start: 0.7626 (tmm) cc_final: 0.7265 (tmm) REVERT: C 105 ASP cc_start: 0.7999 (t0) cc_final: 0.7765 (t0) REVERT: C 114 GLN cc_start: 0.8849 (pp30) cc_final: 0.8386 (pp30) REVERT: C 116 LYS cc_start: 0.5658 (mttp) cc_final: 0.5414 (mttp) outliers start: 28 outliers final: 22 residues processed: 140 average time/residue: 0.1852 time to fit residues: 34.5365 Evaluate side-chains 137 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 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 101 ASN A 145 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6349 Z= 0.184 Angle : 0.658 11.527 8596 Z= 0.308 Chirality : 0.041 0.239 942 Planarity : 0.003 0.025 1047 Dihedral : 4.893 57.259 946 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.89 % Allowed : 21.15 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.31), residues: 761 helix: 0.43 (0.29), residues: 353 sheet: -1.41 (0.55), residues: 97 loop : -1.94 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 204 HIS 0.002 0.001 HIS A 235 PHE 0.026 0.001 PHE C 122 TYR 0.034 0.002 TYR A 358 ARG 0.005 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6150 (mmpt) cc_final: 0.5240 (ptmt) REVERT: A 260 MET cc_start: 0.7608 (tmm) cc_final: 0.7301 (tmt) REVERT: A 464 ARG cc_start: 0.7289 (mmp80) cc_final: 0.4857 (tpp80) REVERT: A 548 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6829 (t80) REVERT: A 567 GLN cc_start: 0.7800 (mp10) cc_final: 0.7419 (mp10) REVERT: B 47 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7182 (mtm-85) REVERT: B 53 MET cc_start: 0.7229 (ttt) cc_final: 0.6993 (ttm) REVERT: C 44 ARG cc_start: 0.7728 (mmm160) cc_final: 0.6901 (mmm160) REVERT: C 102 MET cc_start: 0.7583 (tmm) cc_final: 0.7176 (tmm) REVERT: C 105 ASP cc_start: 0.7980 (t0) cc_final: 0.7714 (t0) outliers start: 25 outliers final: 23 residues processed: 136 average time/residue: 0.1718 time to fit residues: 31.0721 Evaluate side-chains 139 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6349 Z= 0.200 Angle : 0.668 11.667 8596 Z= 0.313 Chirality : 0.041 0.247 942 Planarity : 0.004 0.026 1047 Dihedral : 4.902 57.195 946 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.73 % Allowed : 21.46 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.31), residues: 761 helix: 0.47 (0.29), residues: 353 sheet: -1.40 (0.58), residues: 87 loop : -1.93 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 204 HIS 0.010 0.001 HIS C 100 PHE 0.027 0.001 PHE A 427 TYR 0.034 0.002 TYR A 358 ARG 0.008 0.000 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6151 (mmpt) cc_final: 0.5257 (ptmt) REVERT: A 260 MET cc_start: 0.7623 (tmm) cc_final: 0.7314 (tmt) REVERT: A 301 THR cc_start: 0.7631 (p) cc_final: 0.7413 (p) REVERT: A 464 ARG cc_start: 0.7311 (mmp80) cc_final: 0.4904 (tpp80) REVERT: A 548 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6872 (t80) REVERT: A 567 GLN cc_start: 0.7787 (mp10) cc_final: 0.7416 (mp10) REVERT: B 47 ARG cc_start: 0.7515 (mtm180) cc_final: 0.7211 (mtm-85) REVERT: B 53 MET cc_start: 0.7239 (ttt) cc_final: 0.6877 (ttm) REVERT: C 44 ARG cc_start: 0.7738 (mmm160) cc_final: 0.6902 (mmm160) REVERT: C 105 ASP cc_start: 0.8007 (t0) cc_final: 0.7753 (t0) outliers start: 24 outliers final: 23 residues processed: 134 average time/residue: 0.1724 time to fit residues: 31.0905 Evaluate side-chains 136 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR 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: 0.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.0570 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.147242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112731 restraints weight = 10080.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.116920 restraints weight = 6153.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119804 restraints weight = 4507.927| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.246 6349 Z= 0.327 Angle : 1.072 59.200 8596 Z= 0.608 Chirality : 0.044 0.330 942 Planarity : 0.004 0.061 1047 Dihedral : 5.002 57.194 946 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.35 % Allowed : 21.62 % Favored : 74.03 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.31), residues: 761 helix: 0.54 (0.29), residues: 350 sheet: -1.47 (0.58), residues: 87 loop : -1.88 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 204 HIS 0.006 0.001 HIS C 100 PHE 0.025 0.001 PHE A 427 TYR 0.033 0.002 TYR A 358 ARG 0.003 0.000 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1797.29 seconds wall clock time: 33 minutes 26.48 seconds (2006.48 seconds total)