Starting phenix.real_space_refine on Mon Sep 23 23:13:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/09_2024/7dxi_30910.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/09_2024/7dxi_30910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/09_2024/7dxi_30910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/09_2024/7dxi_30910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/09_2024/7dxi_30910.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/09_2024/7dxi_30910.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Ca 2 9.91 5 S 24 5.16 5 C 3920 2.51 5 N 1064 2.21 5 O 1120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6130 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3064 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 5.74, per 1000 atoms: 0.94 Number of scatterers: 6130 At special positions: 0 Unit cell: (115.333, 115.333, 59.9472, 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) Ca 2 19.99 S 24 16.00 O 1120 8.00 N 1064 7.00 C 3920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 515 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 939.4 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 45.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.560A pdb=" N ILE A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.727A pdb=" N LEU A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.715A pdb=" N ILE A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 5.833A pdb=" N HIS A 164 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 165 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 166 " --> pdb=" O LEU A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 166' Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 349 through 364 removed outlier: 3.750A pdb=" N SER A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.592A pdb=" N LEU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.561A pdb=" N ARG A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 removed outlier: 3.615A pdb=" N MET A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 removed outlier: 3.504A pdb=" N VAL A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 524 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.534A pdb=" N ARG A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 600 removed outlier: 3.932A pdb=" N MET A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 599 " --> pdb=" O PHE A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.560A pdb=" N ILE B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.727A pdb=" N LEU B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.716A pdb=" N ILE B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 5.833A pdb=" N HIS B 164 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 165 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 166' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 349 through 364 removed outlier: 3.749A pdb=" N SER B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.592A pdb=" N LEU B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 428 through 435 Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.561A pdb=" N ARG B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 476 removed outlier: 3.616A pdb=" N MET B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.504A pdb=" N VAL B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.534A pdb=" N ARG B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 566 " --> pdb=" O ARG B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 600 removed outlier: 3.932A pdb=" N MET B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG B 589 " --> pdb=" O ASN B 585 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 599 " --> pdb=" O PHE B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.822A pdb=" N ALA A 66 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL A 120 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR A 68 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 117 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 139 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 119 " --> pdb=" O VAL A 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.822A pdb=" N ALA B 66 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL B 120 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR B 68 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 117 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 139 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE B 119 " --> pdb=" O VAL B 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 174 Processing sheet with id=AA7, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200 168 hydrogen bonds defined for protein. 480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1962 1.34 - 1.46: 1218 1.46 - 1.58: 3066 1.58 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 6286 Sorted by residual: bond pdb=" C GLN B 458 " pdb=" N PRO B 459 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.18e-02 7.18e+03 3.35e+00 bond pdb=" C GLN A 458 " pdb=" N PRO A 459 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.18e-02 7.18e+03 3.26e+00 bond pdb=" CA LYS A 368 " pdb=" C LYS A 368 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.34e-02 5.57e+03 2.55e+00 bond pdb=" CA LYS B 368 " pdb=" C LYS B 368 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.34e-02 5.57e+03 2.52e+00 bond pdb=" N LEU A 176 " pdb=" CA LEU A 176 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.31e-02 5.83e+03 2.34e+00 ... (remaining 6281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 8384 4.00 - 8.01: 125 8.01 - 12.01: 19 12.01 - 16.01: 6 16.01 - 20.01: 2 Bond angle restraints: 8536 Sorted by residual: angle pdb=" C PRO A 459 " pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 125.00 104.99 20.01 4.10e+00 5.95e-02 2.38e+01 angle pdb=" C PRO B 459 " pdb=" N PRO B 460 " pdb=" CD PRO B 460 " ideal model delta sigma weight residual 125.00 104.99 20.01 4.10e+00 5.95e-02 2.38e+01 angle pdb=" CA PRO A 460 " pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 112.00 105.33 6.67 1.40e+00 5.10e-01 2.27e+01 angle pdb=" CA PRO B 460 " pdb=" N PRO B 460 " pdb=" CD PRO B 460 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" N LYS A 368 " pdb=" CA LYS A 368 " pdb=" C LYS A 368 " ideal model delta sigma weight residual 110.80 120.35 -9.55 2.13e+00 2.20e-01 2.01e+01 ... (remaining 8531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3329 17.70 - 35.40: 365 35.40 - 53.11: 62 53.11 - 70.81: 12 70.81 - 88.51: 3 Dihedral angle restraints: 3771 sinusoidal: 1551 harmonic: 2220 Sorted by residual: dihedral pdb=" CA PHE A 367 " pdb=" C PHE A 367 " pdb=" N LYS A 368 " pdb=" CA LYS A 368 " ideal model delta harmonic sigma weight residual -180.00 -128.71 -51.29 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N LYS B 368 " pdb=" CA LYS B 368 " ideal model delta harmonic sigma weight residual -180.00 -128.74 -51.26 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " pdb=" SG CYS A 515 " pdb=" CB CYS A 515 " ideal model delta sinusoidal sigma weight residual 93.00 -178.49 -88.51 1 1.00e+01 1.00e-02 9.35e+01 ... (remaining 3768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 629 0.053 - 0.105: 217 0.105 - 0.158: 63 0.158 - 0.211: 13 0.211 - 0.263: 10 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA LYS A 368 " pdb=" N LYS A 368 " pdb=" C LYS A 368 " pdb=" CB LYS A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA LYS B 368 " pdb=" N LYS B 368 " pdb=" C LYS B 368 " pdb=" CB LYS B 368 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLN B 458 " pdb=" N GLN B 458 " pdb=" C GLN B 458 " pdb=" CB GLN B 458 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 929 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 459 " -0.130 5.00e-02 4.00e+02 1.98e-01 6.27e+01 pdb=" N PRO A 460 " 0.342 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 459 " 0.130 5.00e-02 4.00e+02 1.98e-01 6.25e+01 pdb=" N PRO B 460 " -0.341 5.00e-02 4.00e+02 pdb=" CA PRO B 460 " 0.119 5.00e-02 4.00e+02 pdb=" CD PRO B 460 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 151 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 152 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.065 5.00e-02 4.00e+02 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 3 2.15 - 2.84: 1965 2.84 - 3.53: 7957 3.53 - 4.21: 13695 4.21 - 4.90: 23490 Nonbonded interactions: 47110 Sorted by model distance: nonbonded pdb=" OD2 ASP B 439 " pdb=" OG1 THR B 443 " model vdw 1.468 3.040 nonbonded pdb=" OD2 ASP A 439 " pdb=" OG1 THR A 443 " model vdw 1.468 3.040 nonbonded pdb=" SG CYS B 476 " pdb=" SG CYS B 515 " model vdw 2.034 3.760 nonbonded pdb=" CB ASP A 439 " pdb="CA CA A 701 " model vdw 2.247 2.910 nonbonded pdb=" O THR B 443 " pdb="CA CA B 701 " model vdw 2.248 2.510 ... (remaining 47105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.670 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 0.040 6286 Z= 0.403 Angle : 1.298 20.014 8536 Z= 0.676 Chirality : 0.064 0.263 932 Planarity : 0.012 0.198 1106 Dihedral : 15.064 76.380 2316 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.91 % Favored : 85.54 % Rotamer: Outliers : 0.30 % Allowed : 0.74 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 1.44 % 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: -5.04 (0.24), residues: 726 helix: -3.36 (0.19), residues: 304 sheet: -2.64 (0.75), residues: 36 loop : -3.47 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 463 HIS 0.014 0.002 HIS B 116 PHE 0.052 0.004 PHE B 436 TYR 0.064 0.004 TYR A 175 ARG 0.012 0.001 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6946 (t0) REVERT: A 368 LYS cc_start: 0.6373 (pttp) cc_final: 0.6167 (pttp) REVERT: A 594 ASP cc_start: 0.8115 (t70) cc_final: 0.7628 (m-30) REVERT: B 149 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7037 (t0) REVERT: B 463 TRP cc_start: 0.6358 (p-90) cc_final: 0.6064 (p-90) REVERT: B 589 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7755 (mtp180) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.1926 time to fit residues: 29.6558 Evaluate side-chains 91 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain B residue 149 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 67 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 576 ASN B 116 HIS B 576 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6286 Z= 0.250 Angle : 0.790 12.886 8536 Z= 0.392 Chirality : 0.046 0.160 932 Planarity : 0.009 0.156 1106 Dihedral : 7.997 47.355 834 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.46 % Favored : 84.99 % Rotamer: Outliers : 1.79 % Allowed : 8.04 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.28), residues: 726 helix: -2.18 (0.24), residues: 324 sheet: -2.41 (0.86), residues: 32 loop : -3.15 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 70 HIS 0.004 0.001 HIS A 116 PHE 0.017 0.002 PHE A 595 TYR 0.026 0.002 TYR B 412 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6575 (pm20) REVERT: A 576 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8301 (t0) REVERT: A 594 ASP cc_start: 0.8245 (t70) cc_final: 0.7941 (t0) REVERT: B 576 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8091 (t0) REVERT: B 594 ASP cc_start: 0.8296 (t70) cc_final: 0.8047 (t0) outliers start: 12 outliers final: 6 residues processed: 114 average time/residue: 0.1642 time to fit residues: 25.2970 Evaluate side-chains 99 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 576 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6286 Z= 0.205 Angle : 0.711 8.409 8536 Z= 0.363 Chirality : 0.045 0.185 932 Planarity : 0.007 0.103 1106 Dihedral : 7.626 47.858 834 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.91 % Favored : 85.81 % Rotamer: Outliers : 1.64 % Allowed : 13.54 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.29), residues: 726 helix: -1.57 (0.26), residues: 326 sheet: -3.25 (0.66), residues: 46 loop : -3.03 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 70 HIS 0.002 0.001 HIS A 535 PHE 0.013 0.001 PHE A 595 TYR 0.021 0.001 TYR A 412 ARG 0.003 0.000 ARG B 562 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.786 Fit side-chains REVERT: A 514 ARG cc_start: 0.5507 (ttt180) cc_final: 0.5212 (ptp-110) REVERT: A 554 THR cc_start: 0.7310 (m) cc_final: 0.6606 (m) REVERT: A 558 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6703 (pm20) REVERT: A 594 ASP cc_start: 0.8175 (t70) cc_final: 0.7921 (t0) REVERT: B 150 GLN cc_start: 0.7753 (pt0) cc_final: 0.7540 (pm20) REVERT: B 471 GLU cc_start: 0.6108 (tm-30) cc_final: 0.5884 (tm-30) REVERT: B 576 ASN cc_start: 0.8475 (t0) cc_final: 0.8202 (t0) REVERT: B 594 ASP cc_start: 0.8201 (t70) cc_final: 0.7958 (t0) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 0.1617 time to fit residues: 26.2359 Evaluate side-chains 103 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 526 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6286 Z= 0.262 Angle : 0.741 8.777 8536 Z= 0.380 Chirality : 0.045 0.161 932 Planarity : 0.007 0.104 1106 Dihedral : 7.654 52.437 834 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.33 % Favored : 85.40 % Rotamer: Outliers : 2.38 % Allowed : 15.77 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.29), residues: 726 helix: -1.31 (0.27), residues: 326 sheet: -3.14 (0.68), residues: 42 loop : -3.01 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 444 HIS 0.003 0.001 HIS B 543 PHE 0.014 0.002 PHE B 600 TYR 0.025 0.002 TYR A 412 ARG 0.002 0.000 ARG B 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 514 ARG cc_start: 0.5612 (ttt180) cc_final: 0.5366 (ptp-110) REVERT: A 554 THR cc_start: 0.7358 (m) cc_final: 0.6597 (m) REVERT: A 558 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6626 (pm20) REVERT: A 576 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8227 (t0) REVERT: A 594 ASP cc_start: 0.8149 (t70) cc_final: 0.7909 (t0) REVERT: B 118 TYR cc_start: 0.8774 (m-80) cc_final: 0.8528 (m-80) REVERT: B 150 GLN cc_start: 0.7808 (pt0) cc_final: 0.7567 (pm20) REVERT: B 576 ASN cc_start: 0.8547 (t0) cc_final: 0.8243 (t0) REVERT: B 594 ASP cc_start: 0.8213 (t70) cc_final: 0.7888 (t0) outliers start: 16 outliers final: 12 residues processed: 113 average time/residue: 0.1571 time to fit residues: 24.6350 Evaluate side-chains 111 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6286 Z= 0.297 Angle : 0.752 8.619 8536 Z= 0.387 Chirality : 0.046 0.160 932 Planarity : 0.007 0.106 1106 Dihedral : 7.811 58.792 834 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.74 % Favored : 84.71 % Rotamer: Outliers : 4.61 % Allowed : 15.77 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.29), residues: 726 helix: -1.25 (0.27), residues: 332 sheet: -3.29 (0.66), residues: 42 loop : -3.17 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 444 HIS 0.004 0.001 HIS A 543 PHE 0.015 0.002 PHE B 600 TYR 0.027 0.002 TYR B 412 ARG 0.002 0.000 ARG B 562 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: A 471 GLU cc_start: 0.6067 (tm-30) cc_final: 0.5827 (tm-30) REVERT: A 511 LEU cc_start: 0.8098 (tt) cc_final: 0.7892 (tt) REVERT: A 558 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6663 (pm20) REVERT: A 594 ASP cc_start: 0.8172 (t70) cc_final: 0.7908 (t0) REVERT: B 118 TYR cc_start: 0.8789 (m-80) cc_final: 0.8552 (m-80) REVERT: B 150 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: B 576 ASN cc_start: 0.8486 (t0) cc_final: 0.8237 (t0) REVERT: B 594 ASP cc_start: 0.8206 (t70) cc_final: 0.7891 (t0) outliers start: 31 outliers final: 19 residues processed: 124 average time/residue: 0.1696 time to fit residues: 28.1200 Evaluate side-chains 113 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 563 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6286 Z= 0.198 Angle : 0.701 9.532 8536 Z= 0.359 Chirality : 0.044 0.164 932 Planarity : 0.006 0.105 1106 Dihedral : 7.093 45.870 834 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % Rotamer: Outliers : 2.98 % Allowed : 17.86 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.30), residues: 726 helix: -1.03 (0.27), residues: 338 sheet: -3.05 (0.69), residues: 42 loop : -2.94 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 70 HIS 0.002 0.001 HIS A 535 PHE 0.010 0.001 PHE A 595 TYR 0.019 0.001 TYR B 412 ARG 0.002 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: A 558 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: A 576 ASN cc_start: 0.8352 (t0) cc_final: 0.8021 (t0) REVERT: B 118 TYR cc_start: 0.8752 (m-80) cc_final: 0.8492 (m-80) REVERT: B 150 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: B 467 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7574 (tpp80) REVERT: B 576 ASN cc_start: 0.8470 (t0) cc_final: 0.8172 (t0) REVERT: B 594 ASP cc_start: 0.8119 (t70) cc_final: 0.7894 (t0) outliers start: 20 outliers final: 11 residues processed: 123 average time/residue: 0.1452 time to fit residues: 25.1387 Evaluate side-chains 116 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.4394 > 50: distance: 82 - 100: 26.892 distance: 87 - 106: 16.831 distance: 92 - 114: 28.945 distance: 96 - 100: 28.625 distance: 97 - 122: 25.565 distance: 100 - 101: 11.041 distance: 101 - 102: 27.433 distance: 101 - 104: 13.327 distance: 102 - 103: 29.321 distance: 102 - 106: 29.953 distance: 103 - 133: 17.834 distance: 104 - 105: 36.070 distance: 106 - 107: 31.911 distance: 107 - 108: 25.073 distance: 107 - 110: 20.738 distance: 108 - 109: 41.998 distance: 108 - 114: 9.387 distance: 110 - 111: 13.138 distance: 111 - 112: 14.425 distance: 111 - 113: 26.885 distance: 114 - 115: 21.227 distance: 115 - 116: 35.034 distance: 115 - 118: 25.260 distance: 116 - 117: 22.549 distance: 116 - 122: 27.827 distance: 117 - 152: 24.299 distance: 118 - 119: 32.251 distance: 119 - 120: 8.380 distance: 119 - 121: 7.443 distance: 122 - 123: 25.137 distance: 123 - 124: 29.017 distance: 123 - 126: 27.905 distance: 124 - 125: 26.694 distance: 124 - 133: 14.693 distance: 126 - 127: 37.741 distance: 127 - 128: 33.553 distance: 128 - 129: 25.361 distance: 129 - 130: 9.768 distance: 130 - 131: 15.632 distance: 130 - 132: 19.356 distance: 133 - 134: 30.633 distance: 134 - 135: 39.867 distance: 134 - 137: 42.835 distance: 135 - 136: 24.493 distance: 135 - 141: 28.294 distance: 137 - 138: 52.099 distance: 138 - 139: 35.928 distance: 138 - 140: 21.203 distance: 141 - 142: 21.208 distance: 142 - 143: 21.304 distance: 142 - 145: 40.279 distance: 143 - 144: 14.209 distance: 143 - 152: 21.465 distance: 145 - 146: 35.918 distance: 146 - 147: 18.344 distance: 147 - 148: 10.343 distance: 148 - 149: 8.893 distance: 149 - 150: 10.401 distance: 149 - 151: 8.367 distance: 152 - 153: 15.948 distance: 153 - 154: 34.178 distance: 153 - 156: 23.653 distance: 154 - 155: 32.984 distance: 154 - 163: 18.398 distance: 156 - 157: 20.994 distance: 157 - 158: 12.134 distance: 158 - 159: 11.379 distance: 159 - 160: 5.124 distance: 160 - 161: 4.557 distance: 160 - 162: 4.095 distance: 163 - 164: 48.331 distance: 164 - 165: 14.215 distance: 164 - 167: 25.549 distance: 165 - 166: 25.151 distance: 165 - 171: 10.149 distance: 167 - 168: 25.436 distance: 168 - 169: 13.954 distance: 168 - 170: 6.348 distance: 171 - 172: 35.269 distance: 171 - 177: 32.521 distance: 172 - 173: 30.295 distance: 172 - 175: 26.734 distance: 173 - 174: 45.796 distance: 173 - 178: 36.680 distance: 175 - 176: 44.646 distance: 176 - 177: 30.750 distance: 178 - 179: 38.904 distance: 179 - 180: 59.595 distance: 179 - 182: 39.961 distance: 180 - 181: 34.637 distance: 180 - 189: 28.443 distance: 182 - 183: 60.251 distance: 183 - 184: 16.784 distance: 184 - 185: 34.081 distance: 185 - 186: 18.391 distance: 186 - 187: 21.517 distance: 186 - 188: 11.908