Starting phenix.real_space_refine on Tue Nov 14 23:54:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/11_2023/8opq_17085.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/11_2023/8opq_17085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/11_2023/8opq_17085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/11_2023/8opq_17085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/11_2023/8opq_17085.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/11_2023/8opq_17085.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 38 5.16 5 Cl 2 4.86 5 C 6532 2.51 5 N 1668 2.21 5 O 1766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 538": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10006 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5002 Classifications: {'peptide': 648} Link IDs: {'PTRANS': 28, 'TRANS': 619} Chain breaks: 2 Chain: "B" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5002 Classifications: {'peptide': 648} Link IDs: {'PTRANS': 28, 'TRANS': 619} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.45, per 1000 atoms: 0.54 Number of scatterers: 10006 At special positions: 0 Unit cell: (100.905, 121.737, 106.764, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 38 16.00 O 1766 8.00 N 1668 7.00 C 6532 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: 4.37 Conformation dependent library (CDL) restraints added in 2.0 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 72.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 37 through 46 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 85 through 116 removed outlier: 5.327A pdb=" N LEU A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.715A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.212A pdb=" N GLY A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 4.103A pdb=" N PHE A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 162 Processing helix chain 'A' and resid 170 through 201 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 211 through 236 removed outlier: 4.024A pdb=" N LYS A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 263 through 287 Processing helix chain 'A' and resid 296 through 313 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 340 through 371 removed outlier: 4.798A pdb=" N GLY A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 393 Processing helix chain 'A' and resid 401 through 412 removed outlier: 3.598A pdb=" N GLY A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 4.436A pdb=" N GLY A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.691A pdb=" N PHE A 437 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 removed outlier: 4.058A pdb=" N LEU A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 470 removed outlier: 4.428A pdb=" N LEU A 460 " --> pdb=" O MET A 456 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 487 Processing helix chain 'A' and resid 487 through 509 removed outlier: 3.946A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 565 Processing helix chain 'A' and resid 568 through 594 Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 681 through 698 Processing helix chain 'A' and resid 708 through 718 removed outlier: 3.619A pdb=" N VAL A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 85 through 116 removed outlier: 5.328A pdb=" N LEU B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Proline residue: B 106 - end of helix removed outlier: 3.716A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 removed outlier: 4.212A pdb=" N GLY B 122 " --> pdb=" O PRO B 118 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 123 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 4.103A pdb=" N PHE B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 162 Processing helix chain 'B' and resid 170 through 201 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 211 through 236 removed outlier: 4.023A pdb=" N LYS B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 259 through 262 Processing helix chain 'B' and resid 263 through 287 Processing helix chain 'B' and resid 296 through 313 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 340 through 371 removed outlier: 4.797A pdb=" N GLY B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 393 Processing helix chain 'B' and resid 401 through 412 removed outlier: 3.599A pdb=" N GLY B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 4.436A pdb=" N GLY B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.691A pdb=" N PHE B 437 " --> pdb=" O GLY B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 4.057A pdb=" N LEU B 445 " --> pdb=" O PRO B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 470 removed outlier: 4.427A pdb=" N LEU B 460 " --> pdb=" O MET B 456 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 487 Processing helix chain 'B' and resid 487 through 509 removed outlier: 3.946A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 508 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 565 Processing helix chain 'B' and resid 568 through 594 Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 681 through 698 Processing helix chain 'B' and resid 708 through 718 removed outlier: 3.619A pdb=" N VAL B 712 " --> pdb=" O HIS B 708 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 728 No H-bonds generated for 'chain 'B' and resid 726 through 728' Processing helix chain 'B' and resid 733 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 527 removed outlier: 4.430A pdb=" N VAL A 542 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLN A 518 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N VAL A 540 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS A 541 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP A 673 " --> pdb=" O LYS A 541 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 543 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE A 731 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET A 704 " --> pdb=" O PHE A 731 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AA4, first strand: chain 'B' and resid 525 through 527 removed outlier: 4.431A pdb=" N VAL B 542 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLN B 518 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N VAL B 540 " --> pdb=" O GLN B 518 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS B 541 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP B 673 " --> pdb=" O LYS B 541 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE B 543 " --> pdb=" O ASP B 673 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE B 731 " --> pdb=" O VAL B 702 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N MET B 704 " --> pdb=" O PHE B 731 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1950 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: 3.10 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3163 1.34 - 1.46: 2037 1.46 - 1.58: 4958 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 10220 Sorted by residual: bond pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta sigma weight residual 1.452 1.493 -0.041 1.18e-02 7.18e+03 1.20e+01 bond pdb=" N VAL B 79 " pdb=" CA VAL B 79 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.13e+01 bond pdb=" N LEU B 90 " pdb=" CA LEU B 90 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.17e-02 7.31e+03 6.56e+00 bond pdb=" N CYS B 565 " pdb=" CA CYS B 565 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.31e-02 5.83e+03 6.52e+00 bond pdb=" N ILE B 102 " pdb=" CA ILE B 102 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.19e-02 7.06e+03 6.52e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 311 107.16 - 113.88: 5988 113.88 - 120.59: 4113 120.59 - 127.31: 3372 127.31 - 134.02: 112 Bond angle restraints: 13896 Sorted by residual: angle pdb=" N VAL B 451 " pdb=" CA VAL B 451 " pdb=" C VAL B 451 " ideal model delta sigma weight residual 112.80 108.60 4.20 1.15e+00 7.56e-01 1.33e+01 angle pdb=" N VAL A 451 " pdb=" CA VAL A 451 " pdb=" C VAL A 451 " ideal model delta sigma weight residual 112.80 108.65 4.15 1.15e+00 7.56e-01 1.30e+01 angle pdb=" N ASP B 462 " pdb=" CA ASP B 462 " pdb=" C ASP B 462 " ideal model delta sigma weight residual 111.36 107.46 3.90 1.09e+00 8.42e-01 1.28e+01 angle pdb=" N GLN A 575 " pdb=" CA GLN A 575 " pdb=" C GLN A 575 " ideal model delta sigma weight residual 111.07 107.53 3.54 1.07e+00 8.73e-01 1.10e+01 angle pdb=" N VAL A 79 " pdb=" CA VAL A 79 " pdb=" C VAL A 79 " ideal model delta sigma weight residual 112.96 109.83 3.13 1.00e+00 1.00e+00 9.80e+00 ... (remaining 13891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.56: 5482 11.56 - 23.11: 398 23.11 - 34.67: 128 34.67 - 46.23: 47 46.23 - 57.79: 9 Dihedral angle restraints: 6064 sinusoidal: 2324 harmonic: 3740 Sorted by residual: dihedral pdb=" CA ASP A 736 " pdb=" CB ASP A 736 " pdb=" CG ASP A 736 " pdb=" OD1 ASP A 736 " ideal model delta sinusoidal sigma weight residual -30.00 -87.79 57.79 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP B 736 " pdb=" CB ASP B 736 " pdb=" CG ASP B 736 " pdb=" OD1 ASP B 736 " ideal model delta sinusoidal sigma weight residual -30.00 -87.49 57.49 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ARG A 140 " pdb=" C ARG A 140 " pdb=" N HIS A 141 " pdb=" CA HIS A 141 " ideal model delta harmonic sigma weight residual -180.00 -164.26 -15.74 0 5.00e+00 4.00e-02 9.90e+00 ... (remaining 6061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1243 0.042 - 0.084: 314 0.084 - 0.126: 93 0.126 - 0.168: 15 0.168 - 0.210: 3 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE B 102 " pdb=" N ILE B 102 " pdb=" C ILE B 102 " pdb=" CB ILE B 102 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU A 491 " pdb=" N LEU A 491 " pdb=" C LEU A 491 " pdb=" CB LEU A 491 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 1665 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 64 " 0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ARG B 64 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG B 64 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA B 65 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 537 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C VAL A 537 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL A 537 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 538 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 537 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C VAL B 537 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL B 537 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG B 538 " 0.015 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1941 2.78 - 3.31: 10162 3.31 - 3.84: 16914 3.84 - 4.37: 18453 4.37 - 4.90: 33014 Nonbonded interactions: 80484 Sorted by model distance: nonbonded pdb=" OG SER A 185 " pdb=" O GLY A 391 " model vdw 2.245 2.440 nonbonded pdb=" OG SER B 185 " pdb=" O GLY B 391 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR A 508 " pdb=" OH TYR A 550 " model vdw 2.255 2.440 nonbonded pdb=" OG1 THR B 508 " pdb=" OH TYR B 550 " model vdw 2.255 2.440 nonbonded pdb=" O ALA B 420 " pdb=" OG SER B 423 " model vdw 2.258 2.440 ... (remaining 80479 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 3.600 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: 16.760 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 29.710 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 0.003 0.041 10220 Z= 0.195 Angle : 0.524 6.514 13896 Z= 0.338 Chirality : 0.041 0.210 1668 Planarity : 0.005 0.070 1730 Dihedral : 9.908 57.785 3652 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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: 1.64 (0.25), residues: 1284 helix: 1.55 (0.19), residues: 902 sheet: 0.87 (0.74), residues: 54 loop : -0.01 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2538 time to fit residues: 91.5291 Evaluate side-chains 212 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 394 GLN A 488 ASN A 563 GLN B 104 GLN B 182 GLN B 452 ASN B 563 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.004 0.037 10220 Z= 0.238 Angle : 0.556 10.563 13896 Z= 0.276 Chirality : 0.041 0.144 1668 Planarity : 0.004 0.033 1730 Dihedral : 3.699 15.643 1376 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.91 % Allowed : 13.18 % Favored : 84.91 % 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: 2.26 (0.24), residues: 1284 helix: 2.07 (0.18), residues: 900 sheet: 0.77 (0.74), residues: 54 loop : 0.10 (0.35), residues: 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 236 average time/residue: 0.2372 time to fit residues: 76.8903 Evaluate side-chains 226 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 215 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1176 time to fit residues: 3.7105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 125 optimal weight: 0.2980 chunk 103 optimal weight: 0.0030 chunk 115 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 ASN B 182 GLN B 370 HIS B 563 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10220 Z= 0.193 Angle : 0.529 11.285 13896 Z= 0.258 Chirality : 0.040 0.143 1668 Planarity : 0.004 0.035 1730 Dihedral : 3.731 16.095 1376 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.73 % Allowed : 15.09 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.24), residues: 1284 helix: 2.11 (0.18), residues: 912 sheet: 0.65 (0.73), residues: 54 loop : 0.14 (0.35), residues: 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 1.103 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 250 average time/residue: 0.2466 time to fit residues: 84.5615 Evaluate side-chains 229 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 220 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1379 time to fit residues: 3.6224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 61 optimal weight: 0.0470 chunk 110 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN B 182 GLN B 563 GLN B 664 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10220 Z= 0.231 Angle : 0.534 12.285 13896 Z= 0.263 Chirality : 0.041 0.144 1668 Planarity : 0.004 0.034 1730 Dihedral : 3.772 16.146 1376 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.91 % Allowed : 16.45 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.24), residues: 1284 helix: 2.08 (0.18), residues: 910 sheet: 0.39 (0.70), residues: 54 loop : 0.02 (0.35), residues: 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 1.221 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 243 average time/residue: 0.2373 time to fit residues: 79.7976 Evaluate side-chains 230 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 218 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1056 time to fit residues: 3.8687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 0.0030 chunk 51 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10220 Z= 0.180 Angle : 0.524 12.855 13896 Z= 0.257 Chirality : 0.040 0.154 1668 Planarity : 0.004 0.034 1730 Dihedral : 3.745 16.313 1376 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.64 % Allowed : 17.91 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.24), residues: 1284 helix: 2.13 (0.18), residues: 912 sheet: 0.37 (0.70), residues: 54 loop : 0.10 (0.36), residues: 318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 1.048 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 252 average time/residue: 0.2306 time to fit residues: 79.9752 Evaluate side-chains 242 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 233 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1440 time to fit residues: 3.6076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10220 Z= 0.325 Angle : 0.587 13.136 13896 Z= 0.289 Chirality : 0.043 0.168 1668 Planarity : 0.004 0.035 1730 Dihedral : 3.923 17.103 1376 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.73 % Allowed : 19.00 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.24), residues: 1284 helix: 1.91 (0.18), residues: 910 sheet: 0.25 (0.67), residues: 54 loop : -0.10 (0.36), residues: 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 240 time to evaluate : 1.121 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 249 average time/residue: 0.2442 time to fit residues: 83.1142 Evaluate side-chains 241 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 231 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1341 time to fit residues: 4.0603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10220 Z= 0.202 Angle : 0.567 13.782 13896 Z= 0.272 Chirality : 0.041 0.181 1668 Planarity : 0.004 0.035 1730 Dihedral : 3.863 17.200 1376 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.64 % Allowed : 19.64 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1284 helix: 2.03 (0.18), residues: 908 sheet: 0.31 (0.68), residues: 54 loop : -0.13 (0.36), residues: 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 234 time to evaluate : 1.113 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 241 average time/residue: 0.2269 time to fit residues: 77.0337 Evaluate side-chains 243 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 231 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1004 time to fit residues: 3.7951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10220 Z= 0.283 Angle : 0.607 15.135 13896 Z= 0.292 Chirality : 0.042 0.217 1668 Planarity : 0.004 0.065 1730 Dihedral : 3.945 17.443 1376 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.73 % Allowed : 21.36 % Favored : 77.91 % 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: 1.97 (0.24), residues: 1284 helix: 1.91 (0.18), residues: 906 sheet: 0.18 (0.67), residues: 54 loop : -0.14 (0.36), residues: 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 239 time to evaluate : 1.539 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 244 average time/residue: 0.2549 time to fit residues: 87.5679 Evaluate side-chains 241 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0982 time to fit residues: 2.5314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 121 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN B 182 GLN ** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10220 Z= 0.227 Angle : 0.613 14.676 13896 Z= 0.290 Chirality : 0.042 0.223 1668 Planarity : 0.004 0.061 1730 Dihedral : 3.931 17.443 1376 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.45 % Allowed : 21.55 % Favored : 78.00 % 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: 2.02 (0.24), residues: 1284 helix: 1.96 (0.18), residues: 904 sheet: 0.19 (0.68), residues: 54 loop : -0.14 (0.35), residues: 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 237 time to evaluate : 1.068 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 239 average time/residue: 0.2360 time to fit residues: 78.2334 Evaluate side-chains 239 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1133 time to fit residues: 2.3579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 0.0070 chunk 84 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.0370 chunk 80 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS A 459 GLN A 708 HIS B 708 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10220 Z= 0.201 Angle : 0.612 14.975 13896 Z= 0.289 Chirality : 0.041 0.188 1668 Planarity : 0.004 0.055 1730 Dihedral : 3.876 17.398 1376 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.36 % Allowed : 21.82 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.24), residues: 1284 helix: 2.00 (0.18), residues: 906 sheet: 0.25 (0.68), residues: 54 loop : -0.06 (0.35), residues: 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 229 time to evaluate : 1.140 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 229 average time/residue: 0.2244 time to fit residues: 72.3220 Evaluate side-chains 232 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1016 time to fit residues: 2.2631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119878 restraints weight = 13680.081| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.07 r_work: 0.3395 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10220 Z= 0.214 Angle : 0.614 14.803 13896 Z= 0.291 Chirality : 0.042 0.158 1668 Planarity : 0.004 0.066 1730 Dihedral : 3.892 17.307 1376 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.27 % Allowed : 21.64 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1284 helix: 1.99 (0.18), residues: 906 sheet: 0.19 (0.67), residues: 54 loop : -0.04 (0.35), residues: 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.15 seconds wall clock time: 49 minutes 49.53 seconds (2989.53 seconds total)