Starting phenix.real_space_refine on Wed Feb 14 15:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/02_2024/6tmi_10522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/02_2024/6tmi_10522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/02_2024/6tmi_10522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/02_2024/6tmi_10522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/02_2024/6tmi_10522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/02_2024/6tmi_10522.pdb" } resolution = 3.5 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= 0.004 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: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 3004 2.51 5 N 837 2.21 5 O 904 1.98 5 H 4842 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 58": "OE1" <-> "OE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 109": "OD1" <-> "OD2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 133": "OE1" <-> "OE2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "B ARG 339": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9606 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 327 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "G" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2901 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1688 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Chain: "R" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 754 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "B" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3936 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain breaks: 1 Time building chain proxies: 4.60, per 1000 atoms: 0.48 Number of scatterers: 9606 At special positions: 0 Unit cell: (100.43, 129.48, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 O 904 8.00 N 837 7.00 C 3004 6.00 H 4842 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 72.9% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'C' and resid 54 through 67 removed outlier: 3.727A pdb=" N GLU C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.730A pdb=" N VAL G 96 " --> pdb=" O GLN G 92 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 119 Processing helix chain 'G' and resid 123 through 136 removed outlier: 3.869A pdb=" N ASN G 136 " --> pdb=" O ARG G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 154 Processing helix chain 'G' and resid 159 through 175 Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'G' and resid 236 through 249 removed outlier: 3.866A pdb=" N ARG G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.542A pdb=" N LEU A 24 " --> pdb=" O TRP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 32 through 53 removed outlier: 3.799A pdb=" N TRP A 36 " --> pdb=" O ASN A 32 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 removed outlier: 4.063A pdb=" N TRP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 4.285A pdb=" N CYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 131 removed outlier: 4.376A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 115 removed outlier: 3.997A pdb=" N LEU R 99 " --> pdb=" O TRP R 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.572A pdb=" N THR B 327 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 329 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 346 removed outlier: 3.672A pdb=" N SER B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 402 removed outlier: 4.211A pdb=" N VAL B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA B 352 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 391 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 417 removed outlier: 4.059A pdb=" N ASP B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 439 Processing helix chain 'B' and resid 453 through 471 removed outlier: 4.111A pdb=" N ALA B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.502A pdb=" N ILE B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.864A pdb=" N HIS B 491 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' Processing helix chain 'B' and resid 505 through 521 removed outlier: 3.973A pdb=" N ASN B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 540 through 569 removed outlier: 3.629A pdb=" N GLU B 545 " --> pdb=" O LYS B 541 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE B 546 " --> pdb=" O GLY B 542 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 557 " --> pdb=" O ILE B 553 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 207 through 210 removed outlier: 6.512A pdb=" N GLU G 177 " --> pdb=" O ARG G 209 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 876 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4836 1.03 - 1.23: 7 1.23 - 1.42: 1947 1.42 - 1.62: 2851 1.62 - 1.81: 32 Bond restraints: 9673 Sorted by residual: bond pdb=" CG LEU A 24 " pdb=" CD1 LEU A 24 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.04e+00 bond pdb=" CG LEU A 91 " pdb=" CD2 LEU A 91 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.49e+00 bond pdb=" CB VAL B 342 " pdb=" CG2 VAL B 342 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00 bond pdb=" CB VAL R 114 " pdb=" CG2 VAL R 114 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CB ILE A 90 " pdb=" CG2 ILE A 90 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 ... (remaining 9668 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.77: 77 105.77 - 112.87: 11585 112.87 - 119.97: 2740 119.97 - 127.08: 3081 127.08 - 134.18: 39 Bond angle restraints: 17522 Sorted by residual: angle pdb=" N GLU G 177 " pdb=" CA GLU G 177 " pdb=" C GLU G 177 " ideal model delta sigma weight residual 110.48 113.81 -3.33 1.48e+00 4.57e-01 5.08e+00 angle pdb=" N ILE G 220 " pdb=" CA ILE G 220 " pdb=" C ILE G 220 " ideal model delta sigma weight residual 109.34 113.75 -4.41 2.08e+00 2.31e-01 4.50e+00 angle pdb=" N PRO G 218 " pdb=" CA PRO G 218 " pdb=" C PRO G 218 " ideal model delta sigma weight residual 112.47 108.26 4.21 2.06e+00 2.36e-01 4.18e+00 angle pdb=" N GLY G 222 " pdb=" CA GLY G 222 " pdb=" C GLY G 222 " ideal model delta sigma weight residual 113.18 117.67 -4.49 2.37e+00 1.78e-01 3.59e+00 angle pdb=" N LEU G 157 " pdb=" CA LEU G 157 " pdb=" C LEU G 157 " ideal model delta sigma weight residual 109.81 113.87 -4.06 2.21e+00 2.05e-01 3.38e+00 ... (remaining 17517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3975 17.86 - 35.72: 397 35.72 - 53.57: 90 53.57 - 71.43: 21 71.43 - 89.29: 9 Dihedral angle restraints: 4492 sinusoidal: 2491 harmonic: 2001 Sorted by residual: dihedral pdb=" CA PRO G 218 " pdb=" C PRO G 218 " pdb=" N GLN G 219 " pdb=" CA GLN G 219 " ideal model delta harmonic sigma weight residual 180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA VAL A 49 " pdb=" C VAL A 49 " pdb=" N ILE A 50 " pdb=" CA ILE A 50 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LYS B 324 " pdb=" C LYS B 324 " pdb=" N TYR B 325 " pdb=" CA TYR B 325 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 4489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 438 0.027 - 0.054: 192 0.054 - 0.081: 80 0.081 - 0.107: 33 0.107 - 0.134: 5 Chirality restraints: 748 Sorted by residual: chirality pdb=" CA VAL G 178 " pdb=" N VAL G 178 " pdb=" C VAL G 178 " pdb=" CB VAL G 178 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE G 211 " pdb=" N ILE G 211 " pdb=" C ILE G 211 " pdb=" CB ILE G 211 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CB THR R 108 " pdb=" CA THR R 108 " pdb=" OG1 THR R 108 " pdb=" CG2 THR R 108 " both_signs ideal model delta sigma weight residual False 2.55 2.44 0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 745 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 55 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO C 56 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 402 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO B 403 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 403 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 403 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 42 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C GLY A 42 " 0.036 2.00e-02 2.50e+03 pdb=" O GLY A 42 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 43 " -0.012 2.00e-02 2.50e+03 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 725 2.20 - 2.80: 20923 2.80 - 3.40: 24981 3.40 - 4.00: 31047 4.00 - 4.60: 48715 Nonbonded interactions: 126391 Sorted by model distance: nonbonded pdb=" HH TYR R 126 " pdb=" OD1 ASN B 517 " model vdw 1.605 1.850 nonbonded pdb=" O ARG G 172 " pdb=" H GLY G 176 " model vdw 1.651 1.850 nonbonded pdb=" O ASN G 91 " pdb="HD22 ASN G 91 " model vdw 1.663 1.850 nonbonded pdb=" O SER G 110 " pdb=" HG SER G 111 " model vdw 1.670 1.850 nonbonded pdb=" O GLN G 92 " pdb=" H LYS G 95 " model vdw 1.674 1.850 ... (remaining 126386 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: 14.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 35.070 Check model and map are aligned: 0.190 Set scattering table: 0.090 Process input model: 31.690 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.006 0.047 4831 Z= 0.389 Angle : 0.637 4.905 6510 Z= 0.359 Chirality : 0.038 0.134 748 Planarity : 0.005 0.073 837 Dihedral : 16.160 89.290 1825 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.58 % Allowed : 7.00 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.29), residues: 591 helix: -2.20 (0.21), residues: 423 sheet: -3.67 (1.00), residues: 16 loop : -4.49 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 95 HIS 0.007 0.002 HIS B 499 PHE 0.018 0.002 PHE B 469 TYR 0.011 0.002 TYR B 513 ARG 0.014 0.001 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 ASP cc_start: 0.8047 (m-30) cc_final: 0.7162 (t70) REVERT: R 113 ASP cc_start: 0.8394 (t0) cc_final: 0.7766 (t0) REVERT: B 323 LYS cc_start: 0.4109 (mttp) cc_final: 0.3484 (mttt) REVERT: B 518 ASN cc_start: 0.8346 (m110) cc_final: 0.8139 (m-40) outliers start: 3 outliers final: 1 residues processed: 142 average time/residue: 0.5410 time to fit residues: 92.0473 Evaluate side-chains 80 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN B 526 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4831 Z= 0.226 Angle : 0.611 4.626 6510 Z= 0.328 Chirality : 0.036 0.151 748 Planarity : 0.005 0.072 837 Dihedral : 5.622 31.789 646 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.94 % Favored : 92.89 % Rotamer: Outliers : 2.33 % Allowed : 14.79 % Favored : 82.88 % 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: -2.29 (0.34), residues: 591 helix: -0.55 (0.25), residues: 425 sheet: -3.35 (1.02), residues: 16 loop : -3.95 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.004 0.001 HIS B 499 PHE 0.012 0.002 PHE G 116 TYR 0.007 0.001 TYR G 138 ARG 0.008 0.001 ARG G 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 ASP cc_start: 0.8072 (m-30) cc_final: 0.7027 (t70) REVERT: A 51 GLU cc_start: 0.7691 (pp20) cc_final: 0.7397 (pp20) REVERT: R 113 ASP cc_start: 0.8557 (t0) cc_final: 0.8006 (t0) REVERT: R 119 GLN cc_start: 0.7674 (tp40) cc_final: 0.7325 (tp40) REVERT: B 323 LYS cc_start: 0.4307 (mttp) cc_final: 0.3797 (mttt) REVERT: B 547 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8101 (t) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.3248 time to fit residues: 42.4547 Evaluate side-chains 91 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 547 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4831 Z= 0.185 Angle : 0.534 5.123 6510 Z= 0.284 Chirality : 0.034 0.142 748 Planarity : 0.004 0.067 837 Dihedral : 5.061 30.315 646 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.72 % Allowed : 15.95 % Favored : 81.32 % 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: -1.25 (0.36), residues: 591 helix: 0.30 (0.26), residues: 429 sheet: -3.18 (1.02), residues: 16 loop : -3.97 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE G 167 TYR 0.005 0.001 TYR G 79 ARG 0.004 0.000 ARG G 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 ASP cc_start: 0.8030 (m-30) cc_final: 0.7031 (t70) REVERT: A 53 GLN cc_start: 0.7008 (tp40) cc_final: 0.6756 (mm110) REVERT: R 113 ASP cc_start: 0.8644 (t0) cc_final: 0.8133 (t0) REVERT: B 323 LYS cc_start: 0.4435 (mttp) cc_final: 0.3978 (mttt) REVERT: B 547 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8059 (t) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.3121 time to fit residues: 40.0576 Evaluate side-chains 88 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 547 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4831 Z= 0.188 Angle : 0.535 5.105 6510 Z= 0.286 Chirality : 0.034 0.141 748 Planarity : 0.004 0.067 837 Dihedral : 4.835 30.304 646 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.31 % Allowed : 17.32 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.36), residues: 591 helix: 0.73 (0.26), residues: 429 sheet: -2.82 (0.99), residues: 16 loop : -3.88 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 36 HIS 0.003 0.001 HIS A 73 PHE 0.010 0.001 PHE A 117 TYR 0.006 0.001 TYR G 79 ARG 0.003 0.000 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 ASP cc_start: 0.7945 (m-30) cc_final: 0.6917 (t70) REVERT: G 242 ASP cc_start: 0.8313 (t70) cc_final: 0.8028 (t0) REVERT: R 113 ASP cc_start: 0.8722 (t0) cc_final: 0.8190 (t0) REVERT: B 323 LYS cc_start: 0.4581 (mttp) cc_final: 0.4123 (mttt) REVERT: B 547 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8097 (t) outliers start: 17 outliers final: 14 residues processed: 101 average time/residue: 0.3055 time to fit residues: 41.1335 Evaluate side-chains 103 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 547 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 191 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4831 Z= 0.224 Angle : 0.547 5.120 6510 Z= 0.292 Chirality : 0.034 0.139 748 Planarity : 0.004 0.067 837 Dihedral : 4.692 29.696 646 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.70 % Allowed : 17.70 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.37), residues: 591 helix: 0.96 (0.26), residues: 426 sheet: -2.52 (1.08), residues: 16 loop : -3.83 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.004 0.001 HIS A 73 PHE 0.012 0.001 PHE B 395 TYR 0.005 0.001 TYR B 349 ARG 0.005 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 ASP cc_start: 0.7724 (m-30) cc_final: 0.6841 (t70) REVERT: G 242 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8097 (t0) REVERT: R 113 ASP cc_start: 0.8790 (t0) cc_final: 0.8264 (t0) REVERT: B 323 LYS cc_start: 0.4667 (mttp) cc_final: 0.4221 (mttt) REVERT: B 547 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8165 (t) outliers start: 19 outliers final: 14 residues processed: 106 average time/residue: 0.3050 time to fit residues: 43.5719 Evaluate side-chains 103 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 191 GLN Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 547 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4831 Z= 0.219 Angle : 0.553 5.168 6510 Z= 0.293 Chirality : 0.034 0.140 748 Planarity : 0.004 0.066 837 Dihedral : 4.632 29.185 646 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.31 % Allowed : 19.46 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.37), residues: 591 helix: 1.14 (0.26), residues: 425 sheet: -2.39 (1.17), residues: 16 loop : -3.72 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS A 73 PHE 0.010 0.001 PHE A 117 TYR 0.006 0.001 TYR B 349 ARG 0.002 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 ASP cc_start: 0.7689 (m-30) cc_final: 0.6879 (t70) REVERT: G 242 ASP cc_start: 0.8429 (t70) cc_final: 0.8134 (t0) REVERT: A 53 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7259 (mt0) REVERT: R 113 ASP cc_start: 0.8781 (t0) cc_final: 0.8252 (t0) REVERT: B 547 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8164 (t) outliers start: 17 outliers final: 16 residues processed: 98 average time/residue: 0.2793 time to fit residues: 37.1655 Evaluate side-chains 102 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 547 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4831 Z= 0.153 Angle : 0.509 5.265 6510 Z= 0.266 Chirality : 0.033 0.137 748 Planarity : 0.003 0.064 837 Dihedral : 4.450 28.848 646 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.53 % Allowed : 20.62 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.38), residues: 591 helix: 1.49 (0.27), residues: 423 sheet: -2.33 (1.12), residues: 21 loop : -3.56 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS A 73 PHE 0.012 0.001 PHE A 117 TYR 0.004 0.001 TYR G 79 ARG 0.003 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 ASP cc_start: 0.7624 (m-30) cc_final: 0.6860 (t70) REVERT: G 242 ASP cc_start: 0.8409 (t70) cc_final: 0.8110 (t0) REVERT: A 53 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7308 (mt0) REVERT: R 113 ASP cc_start: 0.8753 (t0) cc_final: 0.8213 (t0) outliers start: 13 outliers final: 11 residues processed: 100 average time/residue: 0.2926 time to fit residues: 39.4187 Evaluate side-chains 96 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 449 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.0470 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4831 Z= 0.161 Angle : 0.518 5.262 6510 Z= 0.272 Chirality : 0.033 0.138 748 Planarity : 0.003 0.063 837 Dihedral : 4.213 19.364 644 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.72 % Allowed : 20.43 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.38), residues: 591 helix: 1.54 (0.27), residues: 424 sheet: -2.09 (1.20), residues: 21 loop : -3.45 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS B 406 PHE 0.012 0.001 PHE B 395 TYR 0.004 0.001 TYR B 349 ARG 0.002 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 242 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8131 (t0) REVERT: A 53 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7331 (mt0) REVERT: R 113 ASP cc_start: 0.8774 (t0) cc_final: 0.8247 (t0) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.2977 time to fit residues: 38.8496 Evaluate side-chains 97 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 354 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4831 Z= 0.158 Angle : 0.509 5.369 6510 Z= 0.267 Chirality : 0.033 0.136 748 Planarity : 0.004 0.063 837 Dihedral : 4.114 18.398 644 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.14 % Allowed : 21.21 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.38), residues: 591 helix: 1.67 (0.27), residues: 424 sheet: -2.11 (1.19), residues: 21 loop : -3.03 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS B 406 PHE 0.011 0.001 PHE A 117 TYR 0.004 0.001 TYR B 399 ARG 0.004 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 242 ASP cc_start: 0.8433 (t70) cc_final: 0.8133 (t0) REVERT: R 113 ASP cc_start: 0.8785 (t0) cc_final: 0.8269 (t0) outliers start: 11 outliers final: 10 residues processed: 96 average time/residue: 0.3255 time to fit residues: 40.9353 Evaluate side-chains 95 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 449 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4831 Z= 0.264 Angle : 0.587 6.432 6510 Z= 0.315 Chirality : 0.035 0.138 748 Planarity : 0.004 0.064 837 Dihedral : 4.243 17.578 644 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.72 % Allowed : 20.82 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.38), residues: 591 helix: 1.41 (0.26), residues: 426 sheet: -2.01 (1.22), residues: 21 loop : -3.25 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.004 0.002 HIS B 406 PHE 0.009 0.001 PHE G 113 TYR 0.011 0.001 TYR B 349 ARG 0.002 0.000 ARG B 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 113 ASP cc_start: 0.8845 (t0) cc_final: 0.8334 (t0) REVERT: B 547 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8210 (t) outliers start: 14 outliers final: 13 residues processed: 97 average time/residue: 0.2936 time to fit residues: 38.5995 Evaluate side-chains 99 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 547 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.097868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.075489 restraints weight = 37036.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.079032 restraints weight = 14136.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.081192 restraints weight = 7462.388| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4831 Z= 0.175 Angle : 0.539 5.522 6510 Z= 0.283 Chirality : 0.033 0.131 748 Planarity : 0.004 0.063 837 Dihedral : 4.118 17.356 644 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.33 % Allowed : 21.40 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.38), residues: 591 helix: 1.60 (0.26), residues: 426 sheet: -1.92 (1.24), residues: 21 loop : -3.13 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.004 0.001 HIS B 406 PHE 0.012 0.001 PHE A 117 TYR 0.009 0.001 TYR G 79 ARG 0.002 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.56 seconds wall clock time: 57 minutes 36.50 seconds (3456.50 seconds total)