Starting phenix.real_space_refine on Fri Mar 15 02:55:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/03_2024/7s9b_24931.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/03_2024/7s9b_24931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/03_2024/7s9b_24931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/03_2024/7s9b_24931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/03_2024/7s9b_24931.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/03_2024/7s9b_24931.pdb" } resolution = 4.2 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6856 2.51 5 N 1680 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10458 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5229 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 644} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 5229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5229 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 644} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.89, per 1000 atoms: 0.56 Number of scatterers: 10458 At special positions: 0 Unit cell: (115.867, 111.615, 117.993, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1872 8.00 N 1680 7.00 C 6856 6.00 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: 4.31 Conformation dependent library (CDL) restraints added in 1.9 seconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 64.3% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.519A pdb=" N LYS A 47 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 removed outlier: 3.617A pdb=" N ILE A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 78 through 105 Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.960A pdb=" N GLY A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 138 through 152 Processing helix chain 'A' and resid 168 through 195 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 206 through 231 removed outlier: 4.203A pdb=" N LYS A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 258 through 282 removed outlier: 3.539A pdb=" N PHE A 282 " --> pdb=" O PHE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 307 removed outlier: 3.585A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 363 removed outlier: 3.724A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.526A pdb=" N GLU A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 406 removed outlier: 4.015A pdb=" N SER A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.226A pdb=" N SER A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 419 " --> pdb=" O CYS A 415 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 424 " --> pdb=" O MET A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.748A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 482 Processing helix chain 'A' and resid 483 through 505 removed outlier: 4.043A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'A' and resid 653 through 671 Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 697 through 702 removed outlier: 4.010A pdb=" N LEU A 702 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 3.644A pdb=" N GLU A 721 " --> pdb=" O GLU A 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.520A pdb=" N LYS B 47 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 removed outlier: 3.616A pdb=" N ILE B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 78 through 105 Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.959A pdb=" N GLY B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 138 through 152 Processing helix chain 'B' and resid 168 through 195 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 206 through 231 removed outlier: 4.201A pdb=" N LYS B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 258 through 282 removed outlier: 3.539A pdb=" N PHE B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 307 removed outlier: 3.584A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 363 removed outlier: 3.723A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE B 346 " --> pdb=" O ASP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.526A pdb=" N GLU B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.937A pdb=" N SER B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.226A pdb=" N SER B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 419 " --> pdb=" O CYS B 415 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 424 " --> pdb=" O MET B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.749A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 482 Processing helix chain 'B' and resid 483 through 505 removed outlier: 4.041A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 653 through 671 Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 697 through 702 removed outlier: 4.011A pdb=" N LEU B 702 " --> pdb=" O LEU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 721 removed outlier: 3.643A pdb=" N GLU B 721 " --> pdb=" O GLU B 717 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 511 through 513 Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 539 removed outlier: 6.622A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 511 through 513 Processing sheet with id=AA4, first strand: chain 'B' and resid 535 through 539 removed outlier: 6.623A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1800 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: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2280 1.33 - 1.45: 2325 1.45 - 1.57: 6007 1.57 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 10694 Sorted by residual: bond pdb=" CB PHE B 351 " pdb=" CG PHE B 351 " ideal model delta sigma weight residual 1.502 1.433 0.069 2.30e-02 1.89e+03 9.05e+00 bond pdb=" CB PHE A 351 " pdb=" CG PHE A 351 " ideal model delta sigma weight residual 1.502 1.434 0.068 2.30e-02 1.89e+03 8.87e+00 bond pdb=" CA SER B 400 " pdb=" CB SER B 400 " ideal model delta sigma weight residual 1.529 1.484 0.045 1.64e-02 3.72e+03 7.48e+00 bond pdb=" CA SER A 400 " pdb=" CB SER A 400 " ideal model delta sigma weight residual 1.528 1.486 0.043 1.66e-02 3.63e+03 6.56e+00 bond pdb=" CD1 PHE A 351 " pdb=" CE1 PHE A 351 " ideal model delta sigma weight residual 1.382 1.307 0.075 3.00e-02 1.11e+03 6.21e+00 ... (remaining 10689 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 320 106.74 - 113.56: 6159 113.56 - 120.39: 4090 120.39 - 127.22: 3883 127.22 - 134.04: 88 Bond angle restraints: 14540 Sorted by residual: angle pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta sigma weight residual 121.54 112.27 9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta sigma weight residual 121.54 112.32 9.22 1.91e+00 2.74e-01 2.33e+01 angle pdb=" C GLU A 404 " pdb=" N GLY A 405 " pdb=" CA GLY A 405 " ideal model delta sigma weight residual 120.14 114.65 5.49 1.25e+00 6.40e-01 1.93e+01 angle pdb=" N LEU A 401 " pdb=" CA LEU A 401 " pdb=" C LEU A 401 " ideal model delta sigma weight residual 111.71 106.99 4.72 1.15e+00 7.56e-01 1.68e+01 angle pdb=" N LEU B 401 " pdb=" CA LEU B 401 " pdb=" C LEU B 401 " ideal model delta sigma weight residual 111.71 107.33 4.38 1.15e+00 7.56e-01 1.45e+01 ... (remaining 14535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 5865 17.04 - 34.08: 399 34.08 - 51.12: 42 51.12 - 68.16: 13 68.16 - 85.20: 7 Dihedral angle restraints: 6326 sinusoidal: 2418 harmonic: 3908 Sorted by residual: dihedral pdb=" CA LYS B 77 " pdb=" C LYS B 77 " pdb=" N GLU B 78 " pdb=" CA GLU B 78 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA LYS A 77 " pdb=" C LYS A 77 " pdb=" N GLU A 78 " pdb=" CA GLU A 78 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA SER A 24 " pdb=" C SER A 24 " pdb=" N HIS A 25 " pdb=" CA HIS A 25 " ideal model delta harmonic sigma weight residual 180.00 154.67 25.33 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 6323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1224 0.047 - 0.093: 407 0.093 - 0.140: 85 0.140 - 0.186: 8 0.186 - 0.233: 4 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CB THR A 390 " pdb=" CA THR A 390 " pdb=" OG1 THR A 390 " pdb=" CG2 THR A 390 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB THR B 390 " pdb=" CA THR B 390 " pdb=" OG1 THR B 390 " pdb=" CG2 THR B 390 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 344 " pdb=" CA ILE A 344 " pdb=" CG1 ILE A 344 " pdb=" CG2 ILE A 344 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 1725 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 396 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C SER A 396 " -0.054 2.00e-02 2.50e+03 pdb=" O SER A 396 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 397 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 396 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C SER B 396 " 0.045 2.00e-02 2.50e+03 pdb=" O SER B 396 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 397 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 330 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO B 331 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " -0.022 5.00e-02 4.00e+02 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1744 2.75 - 3.29: 11763 3.29 - 3.83: 17894 3.83 - 4.36: 19870 4.36 - 4.90: 32512 Nonbonded interactions: 83783 Sorted by model distance: nonbonded pdb=" OD2 ASP B 154 " pdb=" NZ LYS B 235 " model vdw 2.213 2.520 nonbonded pdb=" OD2 ASP A 154 " pdb=" NZ LYS A 235 " model vdw 2.213 2.520 nonbonded pdb=" OE2 GLU A 627 " pdb=" N GLN A 630 " model vdw 2.222 2.520 nonbonded pdb=" OE2 GLU B 627 " pdb=" N GLN B 630 " model vdw 2.223 2.520 nonbonded pdb=" O HIS B 220 " pdb=" OG1 THR B 223 " model vdw 2.243 2.440 ... (remaining 83778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.720 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: 4.220 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.760 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 0.075 10694 Z= 0.399 Angle : 0.824 10.589 14540 Z= 0.477 Chirality : 0.047 0.233 1728 Planarity : 0.005 0.041 1814 Dihedral : 11.725 85.201 3826 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.94 % Favored : 89.76 % Rotamer: Outliers : 0.78 % Allowed : 1.05 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1348 helix: 0.41 (0.18), residues: 828 sheet: -0.21 (0.90), residues: 32 loop : -2.60 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 472 HIS 0.010 0.002 HIS A 25 PHE 0.025 0.002 PHE A 117 TYR 0.027 0.002 TYR A 123 ARG 0.007 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8633 (pp) cc_final: 0.8334 (pp) REVERT: A 267 MET cc_start: 0.8414 (mmt) cc_final: 0.7986 (mmt) REVERT: A 299 MET cc_start: 0.8540 (ppp) cc_final: 0.8189 (ppp) REVERT: A 566 PHE cc_start: 0.7957 (m-80) cc_final: 0.7717 (m-80) REVERT: B 266 LEU cc_start: 0.8631 (pp) cc_final: 0.8397 (pp) REVERT: B 267 MET cc_start: 0.8412 (mmt) cc_final: 0.8062 (mmt) REVERT: B 299 MET cc_start: 0.8561 (ppp) cc_final: 0.8179 (ppp) REVERT: B 566 PHE cc_start: 0.7848 (m-80) cc_final: 0.7620 (m-80) REVERT: B 693 PHE cc_start: 0.8257 (m-10) cc_final: 0.7946 (m-80) outliers start: 9 outliers final: 7 residues processed: 189 average time/residue: 0.1726 time to fit residues: 49.7873 Evaluate side-chains 150 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10694 Z= 0.228 Angle : 0.629 8.407 14540 Z= 0.324 Chirality : 0.043 0.147 1728 Planarity : 0.004 0.035 1814 Dihedral : 4.626 25.304 1450 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.31 % Favored : 91.54 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % 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: -0.40 (0.24), residues: 1348 helix: 0.86 (0.19), residues: 832 sheet: 0.12 (0.87), residues: 32 loop : -2.36 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 472 HIS 0.008 0.001 HIS A 25 PHE 0.015 0.001 PHE A 117 TYR 0.030 0.002 TYR A 340 ARG 0.005 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8642 (pp) cc_final: 0.8389 (pp) REVERT: A 267 MET cc_start: 0.8242 (mmt) cc_final: 0.7902 (mmt) REVERT: A 299 MET cc_start: 0.8593 (ppp) cc_final: 0.8222 (ppp) REVERT: A 453 MET cc_start: 0.9072 (mmt) cc_final: 0.8828 (mmt) REVERT: A 566 PHE cc_start: 0.7989 (m-80) cc_final: 0.7543 (m-80) REVERT: A 693 PHE cc_start: 0.8170 (m-10) cc_final: 0.7903 (m-80) REVERT: B 266 LEU cc_start: 0.8628 (pp) cc_final: 0.8380 (pp) REVERT: B 267 MET cc_start: 0.8336 (mmt) cc_final: 0.7918 (mmt) REVERT: B 299 MET cc_start: 0.8592 (ppp) cc_final: 0.8157 (ppp) REVERT: B 412 LEU cc_start: 0.7393 (mm) cc_final: 0.7178 (mt) REVERT: B 566 PHE cc_start: 0.7926 (m-80) cc_final: 0.7491 (m-80) REVERT: B 693 PHE cc_start: 0.8164 (m-10) cc_final: 0.7908 (m-80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1761 time to fit residues: 49.3150 Evaluate side-chains 150 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS A 29 GLN A 94 GLN A 689 GLN B 25 HIS B 29 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10694 Z= 0.170 Angle : 0.595 7.802 14540 Z= 0.302 Chirality : 0.042 0.164 1728 Planarity : 0.004 0.033 1814 Dihedral : 4.393 27.280 1450 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.27 % Favored : 92.58 % Rotamer: Outliers : 0.17 % Allowed : 4.44 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1348 helix: 1.18 (0.19), residues: 832 sheet: 0.49 (0.92), residues: 32 loop : -2.28 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.006 0.001 HIS A 25 PHE 0.019 0.001 PHE B 111 TYR 0.022 0.001 TYR A 123 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.8235 (m-10) cc_final: 0.7953 (m-10) REVERT: A 207 GLU cc_start: 0.8104 (tt0) cc_final: 0.7706 (tm-30) REVERT: A 267 MET cc_start: 0.8280 (mmt) cc_final: 0.7926 (mmt) REVERT: A 299 MET cc_start: 0.8664 (ppp) cc_final: 0.8291 (ppp) REVERT: A 453 MET cc_start: 0.9024 (mmt) cc_final: 0.8818 (mmt) REVERT: A 469 LEU cc_start: 0.9109 (tp) cc_final: 0.8830 (tp) REVERT: B 198 PHE cc_start: 0.8258 (m-10) cc_final: 0.7914 (m-10) REVERT: B 207 GLU cc_start: 0.7989 (tt0) cc_final: 0.7425 (tm-30) REVERT: B 267 MET cc_start: 0.8334 (mmt) cc_final: 0.7988 (mmt) REVERT: B 299 MET cc_start: 0.8621 (ppp) cc_final: 0.8300 (ppp) REVERT: B 412 LEU cc_start: 0.7447 (mm) cc_final: 0.7211 (mt) REVERT: B 469 LEU cc_start: 0.9065 (tp) cc_final: 0.8796 (tp) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.1694 time to fit residues: 49.5422 Evaluate side-chains 152 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 63 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10694 Z= 0.203 Angle : 0.589 8.297 14540 Z= 0.299 Chirality : 0.043 0.209 1728 Planarity : 0.004 0.048 1814 Dihedral : 4.305 26.280 1450 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.79 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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: 0.11 (0.24), residues: 1348 helix: 1.22 (0.19), residues: 840 sheet: 0.49 (0.91), residues: 32 loop : -2.13 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 472 HIS 0.003 0.001 HIS B 704 PHE 0.014 0.001 PHE B 693 TYR 0.019 0.001 TYR A 123 ARG 0.006 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8311 (tp-100) REVERT: A 198 PHE cc_start: 0.8213 (m-10) cc_final: 0.7981 (m-10) REVERT: A 207 GLU cc_start: 0.8118 (tt0) cc_final: 0.7766 (tm-30) REVERT: A 267 MET cc_start: 0.8332 (mmt) cc_final: 0.7973 (mmt) REVERT: A 299 MET cc_start: 0.8748 (ppp) cc_final: 0.8450 (ppp) REVERT: A 469 LEU cc_start: 0.9128 (tp) cc_final: 0.8856 (tp) REVERT: B 198 PHE cc_start: 0.8191 (m-10) cc_final: 0.7962 (m-10) REVERT: B 207 GLU cc_start: 0.8016 (tt0) cc_final: 0.7530 (tm-30) REVERT: B 267 MET cc_start: 0.8290 (mmt) cc_final: 0.7928 (mmt) REVERT: B 299 MET cc_start: 0.8635 (ppp) cc_final: 0.8286 (ppp) REVERT: B 412 LEU cc_start: 0.7419 (mm) cc_final: 0.7190 (mt) REVERT: B 469 LEU cc_start: 0.9133 (tp) cc_final: 0.8865 (tp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1925 time to fit residues: 53.6789 Evaluate side-chains 150 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10694 Z= 0.157 Angle : 0.589 8.455 14540 Z= 0.295 Chirality : 0.042 0.156 1728 Planarity : 0.004 0.033 1814 Dihedral : 4.251 27.749 1450 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.97 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1348 helix: 1.35 (0.19), residues: 840 sheet: 0.86 (0.92), residues: 32 loop : -2.11 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 472 HIS 0.002 0.001 HIS A 131 PHE 0.013 0.001 PHE B 191 TYR 0.042 0.001 TYR A 123 ARG 0.004 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8958 (mmm) cc_final: 0.8533 (tpp) REVERT: A 198 PHE cc_start: 0.8157 (m-10) cc_final: 0.7905 (m-10) REVERT: A 207 GLU cc_start: 0.7947 (tt0) cc_final: 0.7617 (tm-30) REVERT: A 267 MET cc_start: 0.8332 (mmt) cc_final: 0.7950 (mmt) REVERT: A 299 MET cc_start: 0.8763 (ppp) cc_final: 0.8450 (ppp) REVERT: A 469 LEU cc_start: 0.9107 (tp) cc_final: 0.8872 (tp) REVERT: B 198 PHE cc_start: 0.8180 (m-10) cc_final: 0.7926 (m-10) REVERT: B 207 GLU cc_start: 0.7953 (tt0) cc_final: 0.7487 (tm-30) REVERT: B 267 MET cc_start: 0.8306 (mmt) cc_final: 0.7947 (mmt) REVERT: B 299 MET cc_start: 0.8727 (ppp) cc_final: 0.8429 (ppp) REVERT: B 469 LEU cc_start: 0.9082 (tp) cc_final: 0.8855 (tp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1910 time to fit residues: 53.6219 Evaluate side-chains 151 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 0.0370 chunk 129 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 overall best weight: 1.4860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 365 HIS B 314 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10694 Z= 0.171 Angle : 0.571 8.136 14540 Z= 0.288 Chirality : 0.042 0.152 1728 Planarity : 0.004 0.035 1814 Dihedral : 4.208 26.683 1450 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.86 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1348 helix: 1.34 (0.19), residues: 842 sheet: 0.96 (0.88), residues: 32 loop : -2.03 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 472 HIS 0.002 0.001 HIS B 704 PHE 0.008 0.001 PHE A 191 TYR 0.038 0.001 TYR A 123 ARG 0.006 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9000 (mmm) cc_final: 0.8635 (tpp) REVERT: A 198 PHE cc_start: 0.8100 (m-10) cc_final: 0.7891 (m-10) REVERT: A 207 GLU cc_start: 0.8009 (tt0) cc_final: 0.7631 (tm-30) REVERT: A 267 MET cc_start: 0.8375 (mmt) cc_final: 0.7950 (mmt) REVERT: A 299 MET cc_start: 0.8745 (ppp) cc_final: 0.8440 (ppp) REVERT: A 469 LEU cc_start: 0.9146 (tp) cc_final: 0.8889 (tp) REVERT: B 198 PHE cc_start: 0.8122 (m-10) cc_final: 0.7915 (m-10) REVERT: B 207 GLU cc_start: 0.7987 (tt0) cc_final: 0.7482 (tm-30) REVERT: B 266 LEU cc_start: 0.8545 (pp) cc_final: 0.8343 (pp) REVERT: B 267 MET cc_start: 0.8337 (mmt) cc_final: 0.7951 (mmt) REVERT: B 299 MET cc_start: 0.8778 (ppp) cc_final: 0.8483 (ppp) REVERT: B 469 LEU cc_start: 0.9133 (tp) cc_final: 0.8894 (tp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1827 time to fit residues: 50.8498 Evaluate side-chains 153 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10694 Z= 0.169 Angle : 0.591 7.991 14540 Z= 0.300 Chirality : 0.042 0.176 1728 Planarity : 0.004 0.035 1814 Dihedral : 4.234 26.834 1450 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 0.40 (0.24), residues: 1348 helix: 1.38 (0.19), residues: 844 sheet: 1.06 (0.86), residues: 32 loop : -1.94 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 472 HIS 0.002 0.001 HIS B 704 PHE 0.011 0.001 PHE B 566 TYR 0.032 0.001 TYR A 123 ARG 0.006 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9001 (mmm) cc_final: 0.8656 (tpp) REVERT: A 198 PHE cc_start: 0.8013 (m-10) cc_final: 0.7778 (m-10) REVERT: A 207 GLU cc_start: 0.7951 (tt0) cc_final: 0.7626 (tm-30) REVERT: A 267 MET cc_start: 0.8283 (mmt) cc_final: 0.7910 (mmt) REVERT: A 299 MET cc_start: 0.8712 (ppp) cc_final: 0.8421 (ppp) REVERT: A 382 ASN cc_start: 0.9091 (t0) cc_final: 0.8764 (t0) REVERT: A 469 LEU cc_start: 0.9146 (tp) cc_final: 0.8882 (tp) REVERT: B 84 ILE cc_start: 0.9041 (mm) cc_final: 0.8831 (mm) REVERT: B 198 PHE cc_start: 0.8093 (m-10) cc_final: 0.7878 (m-10) REVERT: B 207 GLU cc_start: 0.7884 (tt0) cc_final: 0.7447 (tm-30) REVERT: B 267 MET cc_start: 0.8343 (mmt) cc_final: 0.7926 (mmt) REVERT: B 299 MET cc_start: 0.8787 (ppp) cc_final: 0.8483 (ppp) REVERT: B 382 ASN cc_start: 0.9108 (t0) cc_final: 0.8797 (t0) REVERT: B 469 LEU cc_start: 0.9144 (tp) cc_final: 0.8911 (tp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1900 time to fit residues: 54.9964 Evaluate side-chains 158 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 117 optimal weight: 0.0870 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 GLN B 59 ASN B 365 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10694 Z= 0.157 Angle : 0.606 8.301 14540 Z= 0.301 Chirality : 0.044 0.249 1728 Planarity : 0.004 0.035 1814 Dihedral : 4.253 26.990 1450 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.64 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1348 helix: 1.37 (0.19), residues: 844 sheet: 1.07 (0.83), residues: 32 loop : -1.86 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 472 HIS 0.001 0.001 HIS A 131 PHE 0.014 0.001 PHE B 351 TYR 0.029 0.001 TYR A 123 ARG 0.005 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9001 (mmm) cc_final: 0.8707 (tpp) REVERT: A 186 THR cc_start: 0.9352 (m) cc_final: 0.9081 (p) REVERT: A 198 PHE cc_start: 0.7980 (m-10) cc_final: 0.7725 (m-10) REVERT: A 207 GLU cc_start: 0.7871 (tt0) cc_final: 0.7548 (tm-30) REVERT: A 266 LEU cc_start: 0.8583 (pp) cc_final: 0.8311 (pp) REVERT: A 267 MET cc_start: 0.8279 (mmt) cc_final: 0.7902 (mmt) REVERT: A 299 MET cc_start: 0.8715 (ppp) cc_final: 0.8414 (ppp) REVERT: A 378 LEU cc_start: 0.9358 (tp) cc_final: 0.9100 (tp) REVERT: A 382 ASN cc_start: 0.9022 (t0) cc_final: 0.8566 (t0) REVERT: A 469 LEU cc_start: 0.9124 (tp) cc_final: 0.8918 (tp) REVERT: B 88 ILE cc_start: 0.8920 (mm) cc_final: 0.8624 (pt) REVERT: B 186 THR cc_start: 0.9343 (m) cc_final: 0.9063 (p) REVERT: B 198 PHE cc_start: 0.7961 (m-10) cc_final: 0.7710 (m-10) REVERT: B 207 GLU cc_start: 0.7874 (tt0) cc_final: 0.7427 (tm-30) REVERT: B 267 MET cc_start: 0.8244 (mmt) cc_final: 0.7874 (mmt) REVERT: B 299 MET cc_start: 0.8776 (ppp) cc_final: 0.8462 (ppp) REVERT: B 378 LEU cc_start: 0.9349 (tp) cc_final: 0.9090 (tp) REVERT: B 382 ASN cc_start: 0.8918 (t0) cc_final: 0.8486 (t0) REVERT: B 469 LEU cc_start: 0.9129 (tp) cc_final: 0.8916 (tp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1790 time to fit residues: 51.4357 Evaluate side-chains 161 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10694 Z= 0.187 Angle : 0.610 8.118 14540 Z= 0.309 Chirality : 0.043 0.228 1728 Planarity : 0.004 0.037 1814 Dihedral : 4.254 26.201 1450 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.09 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.46 (0.25), residues: 1348 helix: 1.42 (0.19), residues: 842 sheet: 1.14 (0.84), residues: 32 loop : -1.89 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 472 HIS 0.002 0.001 HIS B 704 PHE 0.009 0.001 PHE A 111 TYR 0.027 0.001 TYR A 123 ARG 0.006 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9012 (mmm) cc_final: 0.8746 (tpp) REVERT: A 186 THR cc_start: 0.9350 (m) cc_final: 0.9010 (p) REVERT: A 198 PHE cc_start: 0.8024 (m-10) cc_final: 0.7772 (m-10) REVERT: A 207 GLU cc_start: 0.7938 (tt0) cc_final: 0.7586 (tm-30) REVERT: A 266 LEU cc_start: 0.8590 (pp) cc_final: 0.8306 (pp) REVERT: A 267 MET cc_start: 0.8280 (mmt) cc_final: 0.7901 (mmt) REVERT: A 299 MET cc_start: 0.8731 (ppp) cc_final: 0.8429 (ppp) REVERT: A 382 ASN cc_start: 0.9032 (t0) cc_final: 0.8709 (t0) REVERT: A 469 LEU cc_start: 0.9145 (tp) cc_final: 0.8899 (tp) REVERT: B 88 ILE cc_start: 0.8907 (mm) cc_final: 0.8641 (pt) REVERT: B 198 PHE cc_start: 0.8022 (m-10) cc_final: 0.7762 (m-10) REVERT: B 207 GLU cc_start: 0.7899 (tt0) cc_final: 0.7407 (tm-30) REVERT: B 267 MET cc_start: 0.8256 (mmt) cc_final: 0.7871 (mmt) REVERT: B 299 MET cc_start: 0.8791 (ppp) cc_final: 0.8473 (ppp) REVERT: B 469 LEU cc_start: 0.9163 (tp) cc_final: 0.8933 (tp) REVERT: B 508 TYR cc_start: 0.8288 (m-80) cc_final: 0.7999 (m-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1800 time to fit residues: 50.4162 Evaluate side-chains 157 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 82 optimal weight: 0.0770 chunk 65 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10694 Z= 0.150 Angle : 0.601 7.857 14540 Z= 0.300 Chirality : 0.043 0.223 1728 Planarity : 0.004 0.035 1814 Dihedral : 4.274 27.554 1450 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1348 helix: 1.38 (0.18), residues: 844 sheet: 1.33 (0.84), residues: 32 loop : -1.82 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 472 HIS 0.001 0.001 HIS A 131 PHE 0.019 0.001 PHE B 351 TYR 0.026 0.001 TYR A 123 ARG 0.005 0.000 ARG A 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.266 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: A 122 MET cc_start: 0.8967 (mmm) cc_final: 0.8698 (tpp) REVERT: A 186 THR cc_start: 0.9324 (m) cc_final: 0.8969 (p) REVERT: A 207 GLU cc_start: 0.7826 (tt0) cc_final: 0.7532 (tm-30) REVERT: A 266 LEU cc_start: 0.8579 (pp) cc_final: 0.8284 (pp) REVERT: A 267 MET cc_start: 0.8254 (mmt) cc_final: 0.7847 (mmt) REVERT: A 299 MET cc_start: 0.8754 (ppp) cc_final: 0.8448 (ppp) REVERT: A 382 ASN cc_start: 0.8996 (t0) cc_final: 0.8695 (t0) REVERT: B 88 ILE cc_start: 0.8860 (mm) cc_final: 0.8582 (pt) REVERT: B 186 THR cc_start: 0.9355 (m) cc_final: 0.9032 (p) REVERT: B 207 GLU cc_start: 0.7835 (tt0) cc_final: 0.7336 (tm-30) REVERT: B 267 MET cc_start: 0.8242 (mmt) cc_final: 0.7856 (mmt) REVERT: B 299 MET cc_start: 0.8738 (ppp) cc_final: 0.8429 (ppp) REVERT: B 382 ASN cc_start: 0.8791 (t0) cc_final: 0.8528 (t0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1815 time to fit residues: 51.7892 Evaluate side-chains 161 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 9.9990 chunk 98 optimal weight: 0.0980 chunk 15 optimal weight: 0.0370 chunk 29 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 93 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.070780 restraints weight = 39518.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.072778 restraints weight = 21163.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.074054 restraints weight = 13755.532| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10694 Z= 0.168 Angle : 0.597 8.672 14540 Z= 0.296 Chirality : 0.042 0.216 1728 Planarity : 0.004 0.038 1814 Dihedral : 4.184 27.115 1450 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.79 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1348 helix: 1.47 (0.19), residues: 844 sheet: 1.39 (0.84), residues: 32 loop : -1.80 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 472 HIS 0.002 0.001 HIS A 707 PHE 0.011 0.001 PHE B 351 TYR 0.026 0.001 TYR B 114 ARG 0.003 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.61 seconds wall clock time: 36 minutes 29.56 seconds (2189.56 seconds total)