Starting phenix.real_space_refine (version: dev) on Sun Feb 19 17:12:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/02_2023/7s9b_24931.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/02_2023/7s9b_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_24931/02_2023/7s9b_24931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/02_2023/7s9b_24931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/02_2023/7s9b_24931.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9b_24931/02_2023/7s9b_24931.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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-4877/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: 6.32, per 1000 atoms: 0.60 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: 4.27 Conformation dependent library (CDL) restraints added in 1.5 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: 0.45 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: 2.74 Time building geometry restraints manager: 4.57 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 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. 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: 0.620 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: 0.010 Extract box with map and model: 4.460 Check model and map are aligned: 0.140 Process input model: 28.860 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 % 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 *********************** 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 : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 189 average time/residue: 0.1848 time to fit residues: 53.1683 Evaluate side-chains 150 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2314 time to fit residues: 3.7661 ------------------------------------------------------------------------------- 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: 20.0000 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10694 Z= 0.219 Angle : 0.624 8.338 14540 Z= 0.321 Chirality : 0.043 0.147 1728 Planarity : 0.005 0.062 1814 Dihedral : 4.659 27.297 1450 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.31 % Favored : 91.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1348 helix: 0.85 (0.19), residues: 832 sheet: 0.13 (0.87), residues: 32 loop : -2.37 (0.29), residues: 484 *********************** 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 186 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.513 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1820 time to fit residues: 51.4302 Evaluate side-chains 147 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7175 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 97 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS A 29 GLN A 689 GLN B 25 HIS B 29 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 10694 Z= 0.159 Angle : 0.603 7.651 14540 Z= 0.303 Chirality : 0.042 0.172 1728 Planarity : 0.004 0.031 1814 Dihedral : 4.449 27.912 1450 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer Outliers : 0.17 % 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: -0.03 (0.24), residues: 1348 helix: 1.17 (0.19), residues: 836 sheet: 0.57 (0.92), residues: 32 loop : -2.29 (0.29), residues: 480 *********************** 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 : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.1724 time to fit residues: 50.8651 Evaluate side-chains 148 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4722 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1698 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= 0.190 Angle : 0.585 8.394 14540 Z= 0.296 Chirality : 0.043 0.187 1728 Planarity : 0.004 0.035 1814 Dihedral : 4.313 26.475 1450 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.57 % Favored : 92.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1348 helix: 1.24 (0.19), residues: 838 sheet: 0.59 (0.92), residues: 32 loop : -2.15 (0.30), residues: 478 *********************** 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 201 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1984 time to fit residues: 59.3949 Evaluate side-chains 152 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6911 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 314 ASN ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN B 314 ASN B 363 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 10694 Z= 0.267 Angle : 0.639 8.832 14540 Z= 0.327 Chirality : 0.043 0.173 1728 Planarity : 0.004 0.039 1814 Dihedral : 4.380 25.284 1450 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.57 % Favored : 92.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1348 helix: 1.12 (0.19), residues: 842 sheet: 0.47 (0.88), residues: 32 loop : -2.08 (0.30), residues: 474 *********************** 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 : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1968 time to fit residues: 56.6245 Evaluate side-chains 151 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7408 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 0.0870 chunk 31 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- 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** A 504 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10694 Z= 0.200 Angle : 0.605 8.352 14540 Z= 0.307 Chirality : 0.043 0.150 1728 Planarity : 0.004 0.038 1814 Dihedral : 4.367 27.094 1450 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.72 % Favored : 92.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1348 helix: 1.19 (0.19), residues: 842 sheet: 0.60 (0.84), residues: 32 loop : -2.01 (0.30), residues: 474 *********************** 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 193 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2003 time to fit residues: 57.2927 Evaluate side-chains 156 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5994 ------------------------------------------------------------------------------- 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: 8.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN B 29 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 10694 Z= 0.285 Angle : 0.681 10.838 14540 Z= 0.347 Chirality : 0.045 0.201 1728 Planarity : 0.004 0.041 1814 Dihedral : 4.511 25.696 1450 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.16 % Favored : 91.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1348 helix: 1.10 (0.19), residues: 838 sheet: 0.50 (0.83), residues: 32 loop : -1.96 (0.31), residues: 478 *********************** 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 : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1937 time to fit residues: 55.4754 Evaluate side-chains 148 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7085 ------------------------------------------------------------------------------- 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: 9.9990 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1988 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= 0.209 Angle : 0.642 8.458 14540 Z= 0.325 Chirality : 0.045 0.250 1728 Planarity : 0.004 0.040 1814 Dihedral : 4.510 26.585 1450 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.23 % Favored : 91.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1348 helix: 1.15 (0.19), residues: 838 sheet: 0.62 (0.82), residues: 32 loop : -1.87 (0.31), residues: 478 *********************** 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 200 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1990 time to fit residues: 59.3311 Evaluate side-chains 162 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6369 ------------------------------------------------------------------------------- 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: 4.9990 chunk 72 optimal weight: 0.0050 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN B 29 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 10694 Z= 0.162 Angle : 0.621 8.075 14540 Z= 0.314 Chirality : 0.044 0.223 1728 Planarity : 0.004 0.038 1814 Dihedral : 4.456 28.653 1450 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.27 % Favored : 92.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1348 helix: 1.20 (0.18), residues: 842 sheet: 0.93 (0.83), residues: 32 loop : -1.81 (0.31), residues: 474 *********************** 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 202 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2010 time to fit residues: 60.3822 Evaluate side-chains 161 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5971 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 106 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 82 optimal weight: 0.0060 chunk 65 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10694 Z= 0.166 Angle : 0.620 8.430 14540 Z= 0.311 Chirality : 0.043 0.230 1728 Planarity : 0.004 0.039 1814 Dihedral : 4.361 27.095 1450 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.57 % Favored : 92.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1348 helix: 1.26 (0.18), residues: 844 sheet: 1.08 (0.82), residues: 32 loop : -1.75 (0.31), residues: 472 ********************** 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 200 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2040 time to fit residues: 60.7209 Evaluate side-chains 164 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7261 ------------------------------------------------------------------------------- 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: 7.9990 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 0.0060 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 0.0770 chunk 109 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN B 365 HIS B 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071116 restraints weight = 39332.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073047 restraints weight = 21002.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.074305 restraints weight = 13539.807| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2402 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= 0.173 Angle : 0.618 8.762 14540 Z= 0.310 Chirality : 0.043 0.216 1728 Planarity : 0.004 0.039 1814 Dihedral : 4.312 26.641 1450 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1348 helix: 1.29 (0.18), residues: 844 sheet: 1.12 (0.81), residues: 32 loop : -1.70 (0.31), residues: 472 =============================================================================== Job complete usr+sys time: 1955.57 seconds wall clock time: 37 minutes 11.39 seconds (2231.39 seconds total)