Starting phenix.real_space_refine on Sat Dec 9 00:49:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/12_2023/6tmi_10522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/12_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_10522/12_2023/6tmi_10522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/12_2023/6tmi_10522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/12_2023/6tmi_10522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmi_10522/12_2023/6tmi_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.66, per 1000 atoms: 0.49 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: 8.00 Conformation dependent library (CDL) restraints added in 1.0 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: 0.67 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: 3.13 Time building geometry restraints manager: 8.35 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: 3926 17.86 - 35.72: 380 35.72 - 53.57: 75 53.57 - 71.43: 9 71.43 - 89.29: 9 Dihedral angle restraints: 4399 sinusoidal: 2398 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 4396 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: 17.110 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: 0.160 Extract box with map and model: 38.380 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 34.080 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.860 ------------------------------------------------------------------------------- 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 : 0.793 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: 0.4919 time to fit residues: 83.9445 Evaluate side-chains 78 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1137 time to fit residues: 1.2314 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 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: 0.9980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7773 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4831 Z= 0.320 Angle : 0.669 5.438 6510 Z= 0.365 Chirality : 0.038 0.153 748 Planarity : 0.005 0.075 837 Dihedral : 5.601 24.559 644 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.61 % Favored : 92.22 % Rotamer: Outliers : 2.33 % Allowed : 15.18 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.33), residues: 591 helix: -0.70 (0.24), residues: 428 sheet: -3.42 (0.99), residues: 16 loop : -4.16 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.005 0.001 HIS B 499 PHE 0.012 0.002 PHE G 140 TYR 0.006 0.001 TYR B 513 ARG 0.010 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 : 0.706 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: 12 outliers final: 9 residues processed: 99 average time/residue: 0.3260 time to fit residues: 42.1824 Evaluate side-chains 89 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.800 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1211 time to fit residues: 2.8533 ------------------------------------------------------------------------------- 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: 7.9990 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4831 Z= 0.232 Angle : 0.563 5.098 6510 Z= 0.302 Chirality : 0.034 0.134 748 Planarity : 0.004 0.068 837 Dihedral : 5.014 24.288 644 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.17 % Allowed : 17.90 % Favored : 80.93 % 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: -1.33 (0.36), residues: 591 helix: 0.22 (0.26), residues: 429 sheet: -3.06 (1.02), residues: 16 loop : -3.95 (0.50), residues: 146 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 G 167 TYR 0.006 0.001 TYR G 79 ARG 0.004 0.000 ARG B 508 *********************** 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 95 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.834 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: 5 residues processed: 91 average time/residue: 0.2972 time to fit residues: 36.6188 Evaluate side-chains 86 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.808 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1357 time to fit residues: 2.1244 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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: 0.7769 moved from start: 0.4809 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= 0.168 Angle : 0.536 5.168 6510 Z= 0.285 Chirality : 0.033 0.141 748 Planarity : 0.004 0.067 837 Dihedral : 4.706 23.042 644 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.17 % Allowed : 18.48 % Favored : 80.35 % 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: -0.78 (0.36), residues: 591 helix: 0.69 (0.26), residues: 429 sheet: -2.72 (1.04), residues: 16 loop : -3.98 (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 0.011 0.001 PHE A 117 TYR 0.005 0.001 TYR G 79 ARG 0.002 0.000 ARG A 52 *********************** 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 94 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.898 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 outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 0.3204 time to fit residues: 38.9672 Evaluate side-chains 87 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.838 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1409 time to fit residues: 1.8737 ------------------------------------------------------------------------------- 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: 3.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.7883 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4831 Z= 0.285 Angle : 0.585 4.928 6510 Z= 0.317 Chirality : 0.035 0.140 748 Planarity : 0.004 0.069 837 Dihedral : 4.704 21.569 644 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 1.75 % Allowed : 19.26 % Favored : 78.99 % 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: -0.62 (0.37), residues: 591 helix: 0.79 (0.26), residues: 427 sheet: -2.63 (1.09), residues: 16 loop : -3.79 (0.49), residues: 148 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 0.007 0.001 TYR B 349 ARG 0.003 0.000 ARG B 508 *********************** 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 94 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.848 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: 9 outliers final: 5 residues processed: 90 average time/residue: 0.2862 time to fit residues: 34.8662 Evaluate side-chains 88 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.804 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1263 time to fit residues: 2.0664 ------------------------------------------------------------------------------- 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: 1.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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: 0.7873 moved from start: 0.5761 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= 0.208 Angle : 0.543 5.107 6510 Z= 0.289 Chirality : 0.034 0.141 748 Planarity : 0.004 0.066 837 Dihedral : 4.549 20.573 644 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.56 % Allowed : 21.40 % Favored : 77.04 % 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: -0.29 (0.37), residues: 591 helix: 1.06 (0.26), residues: 425 sheet: -2.52 (1.12), residues: 16 loop : -3.71 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.004 0.001 HIS A 73 PHE 0.011 0.001 PHE A 117 TYR 0.005 0.001 TYR B 349 ARG 0.002 0.000 ARG G 203 *********************** 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 98 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.781 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: 8 outliers final: 6 residues processed: 94 average time/residue: 0.3460 time to fit residues: 42.5299 Evaluate side-chains 91 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1308 time to fit residues: 2.3261 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7862 moved from start: 0.6009 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= 0.175 Angle : 0.525 5.173 6510 Z= 0.278 Chirality : 0.033 0.135 748 Planarity : 0.004 0.065 837 Dihedral : 4.391 20.423 644 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.19 % Allowed : 22.18 % Favored : 77.63 % 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: 0.01 (0.37), residues: 591 helix: 1.21 (0.26), residues: 428 sheet: -2.35 (1.22), residues: 16 loop : -3.42 (0.51), residues: 147 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 0.011 0.001 PHE A 117 TYR 0.004 0.001 TYR B 399 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 91 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.807 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: 0 residues processed: 91 average time/residue: 0.3313 time to fit residues: 39.9508 Evaluate side-chains 85 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9662 ------------------------------------------------------------------------------- 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: 4.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 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: 0.7853 moved from start: 0.6228 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= 0.156 Angle : 0.514 5.302 6510 Z= 0.270 Chirality : 0.033 0.137 748 Planarity : 0.003 0.064 837 Dihedral : 4.232 19.360 644 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.58 % Allowed : 22.57 % 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: 0.35 (0.38), residues: 591 helix: 1.43 (0.27), residues: 428 sheet: -2.23 (1.30), residues: 16 loop : -3.21 (0.51), residues: 147 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 0.003 0.001 TYR B 399 ARG 0.002 0.000 ARG G 203 *********************** 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 91 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.842 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: 3 residues processed: 88 average time/residue: 0.3068 time to fit residues: 36.6998 Evaluate side-chains 88 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1483 time to fit residues: 1.7670 ------------------------------------------------------------------------------- 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: 0.8980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7841 moved from start: 0.6311 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= 0.157 Angle : 0.526 7.104 6510 Z= 0.274 Chirality : 0.033 0.135 748 Planarity : 0.003 0.064 837 Dihedral : 4.164 19.085 644 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.39 % Allowed : 23.15 % 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: 0.65 (0.38), residues: 591 helix: 1.60 (0.27), residues: 425 sheet: -1.81 (1.36), residues: 16 loop : -2.87 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.004 0.001 HIS B 406 PHE 0.011 0.001 PHE A 117 TYR 0.010 0.001 TYR G 79 ARG 0.001 0.000 ARG G 240 *********************** 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 89 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.720 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: 2 outliers final: 0 residues processed: 88 average time/residue: 0.2855 time to fit residues: 33.9182 Evaluate side-chains 85 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9940 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4831 Z= 0.192 Angle : 0.537 5.260 6510 Z= 0.283 Chirality : 0.033 0.132 748 Planarity : 0.003 0.065 837 Dihedral : 4.124 18.026 644 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.39 % Allowed : 23.74 % Favored : 75.88 % 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: 0.68 (0.38), residues: 591 helix: 1.64 (0.27), residues: 424 sheet: -1.93 (1.41), residues: 16 loop : -2.86 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.004 0.001 HIS B 406 PHE 0.010 0.001 PHE A 117 TYR 0.006 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 86 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.746 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: 2 outliers final: 2 residues processed: 85 average time/residue: 0.3072 time to fit residues: 35.5224 Evaluate side-chains 84 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1971 time to fit residues: 1.7339 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.097464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074591 restraints weight = 38285.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.078182 restraints weight = 14928.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.080335 restraints weight = 7959.121| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6743 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= 0.210 Angle : 0.553 5.596 6510 Z= 0.294 Chirality : 0.034 0.132 748 Planarity : 0.004 0.065 837 Dihedral : 4.131 17.585 644 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.39 % Allowed : 23.74 % Favored : 75.88 % 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: 0.58 (0.38), residues: 591 helix: 1.58 (0.26), residues: 429 sheet: -2.27 (1.14), residues: 21 loop : -3.07 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.004 0.001 HIS B 406 PHE 0.010 0.001 PHE A 117 TYR 0.006 0.001 TYR B 349 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: 3087.48 seconds wall clock time: 57 minutes 47.02 seconds (3467.02 seconds total)