Starting phenix.real_space_refine (version: dev) on Wed Apr 6 07:37:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/04_2022/6rtc_4997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/04_2022/6rtc_4997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/04_2022/6rtc_4997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/04_2022/6rtc_4997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/04_2022/6rtc_4997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/04_2022/6rtc_4997.pdb" } resolution = 3.96 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 19374 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9687 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 25, 'TRANS': 595} Chain breaks: 2 Chain: "B" Number of atoms: 9687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9687 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 25, 'TRANS': 595} Chain breaks: 2 Time building chain proxies: 9.42, per 1000 atoms: 0.49 Number of scatterers: 19374 At special positions: 0 Unit cell: (97.825, 121.475, 121.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 1680 8.00 N 1536 7.00 C 6286 6.00 H 9804 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.74 Conformation dependent library (CDL) restraints added in 1.8 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 7 sheets defined 63.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 70 through 95 Proline residue: A 87 - end of helix removed outlier: 4.060A pdb=" N MET A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 118 Proline residue: A 110 - end of helix removed outlier: 4.160A pdb=" N THR A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 removed outlier: 3.646A pdb=" N SER A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 191 Processing helix chain 'A' and resid 200 through 225 removed outlier: 4.198A pdb=" N LYS A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 removed outlier: 4.070A pdb=" N PHE A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 removed outlier: 3.671A pdb=" N TYR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 333 through 360 removed outlier: 3.549A pdb=" N ALA A 337 " --> pdb=" O MET A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 380 removed outlier: 3.857A pdb=" N ILE A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.556A pdb=" N GLY A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.671A pdb=" N VAL A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 4.343A pdb=" N LEU A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 450 through 457 removed outlier: 4.221A pdb=" N TYR A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 removed outlier: 4.284A pdb=" N CYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 498 removed outlier: 4.399A pdb=" N ALA A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.729A pdb=" N THR A 519 " --> pdb=" O ASN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.661A pdb=" N ALA A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 676 through 692 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.657A pdb=" N TYR A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 removed outlier: 3.782A pdb=" N ALA A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 70 through 95 Proline residue: B 87 - end of helix removed outlier: 4.060A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 Proline residue: B 110 - end of helix removed outlier: 4.161A pdb=" N THR B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 removed outlier: 3.646A pdb=" N SER B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 191 Processing helix chain 'B' and resid 200 through 225 removed outlier: 4.199A pdb=" N LYS B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 247 removed outlier: 4.069A pdb=" N PHE B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.671A pdb=" N TYR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 333 through 360 removed outlier: 3.549A pdb=" N ALA B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 removed outlier: 3.857A pdb=" N ILE B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.556A pdb=" N GLY B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.670A pdb=" N VAL B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 removed outlier: 4.343A pdb=" N LEU B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 449 Processing helix chain 'B' and resid 450 through 457 removed outlier: 4.221A pdb=" N TYR B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 removed outlier: 4.284A pdb=" N CYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 498 removed outlier: 4.399A pdb=" N ALA B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.729A pdb=" N THR B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 542 through 552 removed outlier: 3.661A pdb=" N ALA B 552 " --> pdb=" O GLN B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 676 through 692 Processing helix chain 'B' and resid 703 through 712 removed outlier: 3.657A pdb=" N TYR B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 removed outlier: 3.782A pdb=" N ALA B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 740 " --> pdb=" O PHE B 736 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.582A pdb=" N TYR A 159 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 507 Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 533 removed outlier: 6.920A pdb=" N LYS A 530 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP A 668 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A 532 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 665 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 700 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 667 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N PHE A 727 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 699 " --> pdb=" O PHE A 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.582A pdb=" N TYR B 159 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 506 through 507 Processing sheet with id=AA7, first strand: chain 'B' and resid 530 through 533 removed outlier: 6.920A pdb=" N LYS B 530 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP B 668 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL B 532 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 665 " --> pdb=" O PHE B 698 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL B 700 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 667 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N PHE B 727 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU B 699 " --> pdb=" O PHE B 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 506 hydrogen bonds defined for protein. 1482 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: 6.68 Time building geometry restraints manager: 16.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9776 1.03 - 1.22: 30 1.22 - 1.42: 4060 1.42 - 1.62: 5624 1.62 - 1.82: 108 Bond restraints: 19598 Sorted by residual: bond pdb=" CG LEU B 340 " pdb=" CD1 LEU B 340 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CG LEU A 340 " pdb=" CD1 LEU A 340 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.50e+00 bond pdb=" CB PRO A 537 " pdb=" CG PRO A 537 " ideal model delta sigma weight residual 1.492 1.399 0.093 5.00e-02 4.00e+02 3.46e+00 bond pdb=" CB PRO B 537 " pdb=" CG PRO B 537 " ideal model delta sigma weight residual 1.492 1.399 0.093 5.00e-02 4.00e+02 3.46e+00 bond pdb=" CG1 ILE A 387 " pdb=" CD1 ILE A 387 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.70e+00 ... (remaining 19593 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.44: 538 106.44 - 113.43: 23032 113.43 - 120.42: 6928 120.42 - 127.41: 4912 127.41 - 134.40: 92 Bond angle restraints: 35502 Sorted by residual: angle pdb=" CD1 LEU B 538 " pdb=" CG LEU B 538 " pdb=" CD2 LEU B 538 " ideal model delta sigma weight residual 110.80 104.18 6.62 2.20e+00 2.07e-01 9.06e+00 angle pdb=" CD1 LEU A 538 " pdb=" CG LEU A 538 " pdb=" CD2 LEU A 538 " ideal model delta sigma weight residual 110.80 104.20 6.60 2.20e+00 2.07e-01 8.99e+00 angle pdb=" CA LEU A 538 " pdb=" CB LEU A 538 " pdb=" CG LEU A 538 " ideal model delta sigma weight residual 116.30 125.99 -9.69 3.50e+00 8.16e-02 7.66e+00 angle pdb=" N GLY B 193 " pdb=" CA GLY B 193 " pdb=" C GLY B 193 " ideal model delta sigma weight residual 113.18 119.74 -6.56 2.37e+00 1.78e-01 7.65e+00 angle pdb=" CA LEU B 538 " pdb=" CB LEU B 538 " pdb=" CG LEU B 538 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.65e+00 ... (remaining 35497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 6838 16.13 - 32.25: 828 32.25 - 48.38: 168 48.38 - 64.50: 24 64.50 - 80.63: 10 Dihedral angle restraints: 7868 sinusoidal: 3512 harmonic: 4356 Sorted by residual: dihedral pdb=" CA PHE B 662 " pdb=" C PHE B 662 " pdb=" N HIS B 663 " pdb=" CA HIS B 663 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA PHE A 662 " pdb=" C PHE A 662 " pdb=" N HIS A 663 " pdb=" CA HIS A 663 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA PHE A 108 " pdb=" C PHE A 108 " pdb=" N PHE A 109 " pdb=" CA PHE A 109 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 7865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1437 0.089 - 0.178: 121 0.178 - 0.267: 4 0.267 - 0.356: 0 0.356 - 0.445: 2 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CG LEU B 340 " pdb=" CB LEU B 340 " pdb=" CD1 LEU B 340 " pdb=" CD2 LEU B 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CG LEU A 340 " pdb=" CB LEU A 340 " pdb=" CD1 LEU A 340 " pdb=" CD2 LEU A 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1561 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 536 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 537 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 537 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 537 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 536 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO A 537 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 537 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 537 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 228 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO A 229 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.032 5.00e-02 4.00e+02 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 3745 2.29 - 2.87: 42627 2.87 - 3.45: 47241 3.45 - 4.02: 62540 4.02 - 4.60: 96516 Nonbonded interactions: 252669 Sorted by model distance: nonbonded pdb=" HH TYR B 345 " pdb=" O SER B 365 " model vdw 1.716 1.850 nonbonded pdb=" HH TYR A 345 " pdb=" O SER A 365 " model vdw 1.716 1.850 nonbonded pdb=" O GLN A 405 " pdb=" HG SER A 408 " model vdw 1.718 1.850 nonbonded pdb=" O GLN B 405 " pdb=" HG SER B 408 " model vdw 1.718 1.850 nonbonded pdb=" HH TYR B 114 " pdb=" OE2 GLU B 368 " model vdw 1.720 1.850 ... (remaining 252664 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: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 6286 2.51 5 N 1536 2.21 5 O 1680 1.98 5 H 9804 0.53 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=0.50 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: 0.570 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: 0.300 Extract box with map and model: 4.360 Check model and map are aligned: 0.280 Convert atoms to be neutral: 0.180 Process input model: 58.860 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.007 0.093 9794 Z= 0.461 Angle : 0.910 9.688 13294 Z= 0.479 Chirality : 0.051 0.445 1564 Planarity : 0.007 0.072 1646 Dihedral : 14.958 80.630 3450 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: -3.83 (0.19), residues: 1230 helix: -1.98 (0.15), residues: 708 sheet: -3.02 (0.54), residues: 38 loop : -3.26 (0.25), residues: 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3719 time to fit residues: 109.8717 Evaluate side-chains 124 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 273 ASN A 542 ASN B 122 GLN B 273 ASN B 542 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 9794 Z= 0.183 Angle : 0.560 6.746 13294 Z= 0.301 Chirality : 0.039 0.133 1564 Planarity : 0.004 0.039 1646 Dihedral : 4.709 21.663 1314 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.96 % Favored : 94.88 % Rotamer Outliers : 1.71 % 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: -1.41 (0.24), residues: 1230 helix: 0.23 (0.19), residues: 720 sheet: -2.02 (0.65), residues: 52 loop : -2.72 (0.28), residues: 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 157 average time/residue: 0.3393 time to fit residues: 82.9654 Evaluate side-chains 141 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2017 time to fit residues: 4.2552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 273 ASN A 367 GLN B 121 HIS B 273 ASN B 367 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.048 9794 Z= 0.522 Angle : 0.720 6.877 13294 Z= 0.404 Chirality : 0.044 0.175 1564 Planarity : 0.005 0.040 1646 Dihedral : 5.115 21.092 1314 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.67 % Favored : 93.17 % Rotamer Outliers : 2.19 % 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: -1.32 (0.23), residues: 1230 helix: 0.32 (0.19), residues: 720 sheet: -2.08 (0.71), residues: 38 loop : -2.71 (0.27), residues: 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 163 average time/residue: 0.3177 time to fit residues: 82.9699 Evaluate side-chains 153 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2128 time to fit residues: 6.5723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 119 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9794 Z= 0.151 Angle : 0.527 6.467 13294 Z= 0.280 Chirality : 0.039 0.130 1564 Planarity : 0.003 0.029 1646 Dihedral : 4.470 20.127 1314 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.28 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1230 helix: 1.15 (0.20), residues: 712 sheet: -1.73 (0.69), residues: 52 loop : -2.32 (0.29), residues: 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 155 average time/residue: 0.3340 time to fit residues: 82.1440 Evaluate side-chains 151 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1957 time to fit residues: 4.8967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9794 Z= 0.191 Angle : 0.530 6.549 13294 Z= 0.282 Chirality : 0.039 0.130 1564 Planarity : 0.003 0.030 1646 Dihedral : 4.306 20.078 1314 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.61 % Favored : 94.23 % Rotamer Outliers : 1.14 % 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: -0.27 (0.25), residues: 1230 helix: 1.22 (0.20), residues: 724 sheet: -1.73 (0.70), residues: 52 loop : -2.40 (0.29), residues: 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 151 average time/residue: 0.3211 time to fit residues: 77.0910 Evaluate side-chains 143 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2254 time to fit residues: 3.1872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9794 Z= 0.261 Angle : 0.555 6.657 13294 Z= 0.299 Chirality : 0.039 0.144 1564 Planarity : 0.003 0.032 1646 Dihedral : 4.333 19.649 1314 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.50 % Favored : 93.33 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1230 helix: 1.16 (0.19), residues: 724 sheet: -1.78 (0.70), residues: 52 loop : -2.42 (0.29), residues: 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 145 average time/residue: 0.3387 time to fit residues: 78.2594 Evaluate side-chains 140 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.699 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2528 time to fit residues: 5.5433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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: 0.8064 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9794 Z= 0.157 Angle : 0.508 6.512 13294 Z= 0.268 Chirality : 0.038 0.145 1564 Planarity : 0.003 0.030 1646 Dihedral : 4.122 19.011 1314 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.61 % Favored : 94.23 % Rotamer Outliers : 0.76 % 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 (0.25), residues: 1230 helix: 1.48 (0.20), residues: 722 sheet: -1.65 (0.69), residues: 52 loop : -2.29 (0.30), residues: 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 146 average time/residue: 0.3345 time to fit residues: 77.7830 Evaluate side-chains 141 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2157 time to fit residues: 4.3722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 0.0980 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 9794 Z= 0.146 Angle : 0.497 6.485 13294 Z= 0.261 Chirality : 0.038 0.169 1564 Planarity : 0.003 0.029 1646 Dihedral : 3.975 18.529 1314 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 1.05 % 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: 0.28 (0.25), residues: 1230 helix: 1.68 (0.20), residues: 722 sheet: -1.52 (0.69), residues: 52 loop : -2.19 (0.30), residues: 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 156 average time/residue: 0.3427 time to fit residues: 86.1348 Evaluate side-chains 145 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2186 time to fit residues: 5.0331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8053 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 9794 Z= 0.162 Angle : 0.507 6.488 13294 Z= 0.266 Chirality : 0.039 0.183 1564 Planarity : 0.003 0.030 1646 Dihedral : 3.923 18.419 1314 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 0.48 % 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 (0.25), residues: 1230 helix: 1.78 (0.20), residues: 718 sheet: -1.48 (0.69), residues: 52 loop : -2.08 (0.30), residues: 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 149 average time/residue: 0.3209 time to fit residues: 76.7555 Evaluate side-chains 149 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2004 time to fit residues: 3.8253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.8100 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 9794 Z= 0.248 Angle : 0.549 6.578 13294 Z= 0.294 Chirality : 0.039 0.206 1564 Planarity : 0.003 0.030 1646 Dihedral : 4.057 18.800 1314 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.76 % Rotamer Outliers : 0.19 % 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: 0.23 (0.25), residues: 1230 helix: 1.62 (0.19), residues: 718 sheet: -1.52 (0.68), residues: 52 loop : -2.13 (0.30), residues: 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 139 average time/residue: 0.3331 time to fit residues: 73.7037 Evaluate side-chains 139 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1968 time to fit residues: 2.9089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.0770 chunk 86 optimal weight: 2.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS B 731 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.102739 restraints weight = 45063.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106941 restraints weight = 22833.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109730 restraints weight = 15436.203| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 9794 Z= 0.135 Angle : 0.505 6.468 13294 Z= 0.262 Chirality : 0.039 0.182 1564 Planarity : 0.003 0.029 1646 Dihedral : 3.835 18.115 1314 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.19 % 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: 0.77 (0.25), residues: 1230 helix: 2.11 (0.20), residues: 706 sheet: -1.36 (0.69), residues: 52 loop : -1.88 (0.30), residues: 472 =============================================================================== Job complete usr+sys time: 3541.66 seconds wall clock time: 63 minutes 53.02 seconds (3833.02 seconds total)