Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 11:20:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/04_2023/6tmi_10522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/04_2023/6tmi_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_10522/04_2023/6tmi_10522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/04_2023/6tmi_10522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/04_2023/6tmi_10522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/04_2023/6tmi_10522.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 4.76, per 1000 atoms: 0.50 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: 7.69 Conformation dependent library (CDL) restraints added in 945.6 milliseconds 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: 0.19 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: 3.17 Time building geometry restraints manager: 7.96 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: 3424 17.86 - 35.72: 362 35.72 - 53.57: 65 53.57 - 71.43: 8 71.43 - 89.29: 9 Dihedral angle restraints: 3868 sinusoidal: 1867 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 3865 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: 10.360 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: 0.140 Extract box with map and model: 35.520 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.990 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.070 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.861 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 outliers start: 3 outliers final: 1 residues processed: 142 average time/residue: 0.5039 time to fit residues: 86.2272 Evaluate side-chains 78 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1118 time to fit residues: 1.2539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 4831 Z= 0.255 Angle : 0.615 4.861 6510 Z= 0.333 Chirality : 0.036 0.151 748 Planarity : 0.005 0.075 837 Dihedral : 5.600 24.987 644 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 2.14 % 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: -2.56 (0.33), residues: 591 helix: -0.75 (0.24), residues: 428 sheet: -3.40 (1.01), residues: 16 loop : -4.10 (0.48), residues: 147 *********************** 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 96 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.813 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 outliers start: 11 outliers final: 9 residues processed: 95 average time/residue: 0.3254 time to fit residues: 40.3896 Evaluate side-chains 87 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.758 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1088 time to fit residues: 2.6982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4831 Z= 0.173 Angle : 0.535 5.242 6510 Z= 0.284 Chirality : 0.034 0.142 748 Planarity : 0.004 0.068 837 Dihedral : 4.931 24.637 644 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 0.97 % 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 (0.36), residues: 591 helix: 0.31 (0.26), residues: 425 sheet: -3.11 (1.03), residues: 16 loop : -3.78 (0.48), residues: 150 *********************** 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 90 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.935 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 outliers start: 5 outliers final: 3 residues processed: 87 average time/residue: 0.2927 time to fit residues: 34.2319 Evaluate side-chains 82 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.830 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1288 time to fit residues: 1.7376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7809 moved from start: 0.4681 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= 0.222 Angle : 0.557 4.902 6510 Z= 0.303 Chirality : 0.034 0.148 748 Planarity : 0.004 0.072 837 Dihedral : 4.682 22.063 644 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 2.14 % 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: -0.72 (0.36), residues: 591 helix: 0.71 (0.26), residues: 430 sheet: -2.73 (0.95), residues: 16 loop : -3.89 (0.50), residues: 145 *********************** 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 101 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.818 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 outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.3325 time to fit residues: 41.0442 Evaluate side-chains 91 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.787 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2166 time to fit residues: 3.8091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7779 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 4831 Z= 0.157 Angle : 0.522 5.295 6510 Z= 0.275 Chirality : 0.033 0.137 748 Planarity : 0.004 0.068 837 Dihedral : 4.444 21.754 644 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 1.17 % 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: -0.21 (0.37), residues: 591 helix: 1.07 (0.26), residues: 429 sheet: -2.43 (1.08), residues: 16 loop : -3.65 (0.50), residues: 146 *********************** 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 95 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 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: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 93 average time/residue: 0.3324 time to fit residues: 40.4322 Evaluate side-chains 84 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1307 time to fit residues: 1.4273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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: 0.7778 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 4831 Z= 0.153 Angle : 0.515 5.361 6510 Z= 0.268 Chirality : 0.033 0.139 748 Planarity : 0.004 0.067 837 Dihedral : 4.276 20.981 644 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 0.58 % 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: 1.37 (0.26), residues: 429 sheet: -2.29 (1.19), residues: 16 loop : -3.46 (0.51), residues: 146 *********************** 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 90 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.742 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 outliers start: 3 outliers final: 2 residues processed: 88 average time/residue: 0.3172 time to fit residues: 38.0751 Evaluate side-chains 82 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1359 time to fit residues: 1.5107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.5643 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= 0.173 Angle : 0.516 5.321 6510 Z= 0.272 Chirality : 0.033 0.139 748 Planarity : 0.003 0.066 837 Dihedral : 4.209 19.841 644 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.97 % 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 (0.38), residues: 591 helix: 1.52 (0.27), residues: 426 sheet: -2.10 (1.30), residues: 16 loop : -3.22 (0.50), residues: 149 *********************** 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 94 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.923 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 outliers start: 5 outliers final: 3 residues processed: 91 average time/residue: 0.3018 time to fit residues: 36.8554 Evaluate side-chains 87 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1993 time to fit residues: 1.8607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 49 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4831 Z= 0.147 Angle : 0.508 5.364 6510 Z= 0.266 Chirality : 0.032 0.137 748 Planarity : 0.003 0.065 837 Dihedral : 4.089 19.494 644 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 0.19 % 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: 0.69 (0.38), residues: 591 helix: 1.68 (0.27), residues: 424 sheet: -2.12 (1.37), residues: 16 loop : -2.94 (0.53), residues: 151 *********************** 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 88 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.859 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 outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 0.3319 time to fit residues: 38.0216 Evaluate side-chains 82 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1372 time to fit residues: 1.1870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4831 Z= 0.168 Angle : 0.521 5.331 6510 Z= 0.273 Chirality : 0.033 0.137 748 Planarity : 0.004 0.066 837 Dihedral : 4.035 18.797 644 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.00 % 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 (0.38), residues: 591 helix: 1.67 (0.27), residues: 427 sheet: -2.02 (1.37), residues: 16 loop : -2.98 (0.51), residues: 148 *********************** 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 85 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.831 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 outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3202 time to fit residues: 36.3289 Evaluate side-chains 83 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4831 Z= 0.154 Angle : 0.509 5.401 6510 Z= 0.268 Chirality : 0.033 0.133 748 Planarity : 0.004 0.064 837 Dihedral : 3.935 17.909 644 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.19 % 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: 0.85 (0.38), residues: 591 helix: 1.79 (0.26), residues: 427 sheet: -2.30 (1.14), residues: 21 loop : -2.91 (0.53), residues: 143 ********************** 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 89 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.786 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 outliers start: 1 outliers final: 1 residues processed: 88 average time/residue: 0.3378 time to fit residues: 39.1383 Evaluate side-chains 86 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1488 time to fit residues: 1.3381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 201 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** 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 = 0.3786 r_free = 0.3786 target = 0.097116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074777 restraints weight = 37536.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.078235 restraints weight = 14771.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.080322 restraints weight = 7886.882| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 4831 Z= 0.266 Angle : 0.571 5.335 6510 Z= 0.306 Chirality : 0.035 0.135 748 Planarity : 0.004 0.067 837 Dihedral : 4.056 17.371 644 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 0.19 % 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: 0.56 (0.37), residues: 591 helix: 1.56 (0.26), residues: 427 sheet: -2.31 (1.14), residues: 21 loop : -2.99 (0.52), residues: 143 =============================================================================== Job complete usr+sys time: 3011.84 seconds wall clock time: 54 minutes 4.41 seconds (3244.41 seconds total)