Starting phenix.real_space_refine on Sun Mar 17 23:18:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/03_2024/6rtc_4997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/03_2024/6rtc_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_4997/03_2024/6rtc_4997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/03_2024/6rtc_4997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/03_2024/6rtc_4997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/03_2024/6rtc_4997.pdb" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 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. 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-5265/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: 8.89, per 1000 atoms: 0.46 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: 15.08 Conformation dependent library (CDL) restraints added in 2.0 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: 1.49 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: 6.46 Time building geometry restraints manager: 15.74 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: 7992 16.13 - 32.25: 916 32.25 - 48.38: 244 48.38 - 64.50: 108 64.50 - 80.63: 10 Dihedral angle restraints: 9270 sinusoidal: 4914 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 9267 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 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: 1.140 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: 0.290 Extract box with map and model: 3.800 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 60.770 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 % Allowed : 4.19 % Favored : 95.81 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 61 HIS 0.005 0.002 HIS A 712 PHE 0.020 0.002 PHE A 546 TYR 0.027 0.002 TYR A 690 ARG 0.002 0.000 ARG B 457 *********************** 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 : 1.637 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 REVERT: A 115 PHE cc_start: 0.8527 (t80) cc_final: 0.8273 (t80) REVERT: A 123 MET cc_start: 0.8382 (ptm) cc_final: 0.8128 (ptt) REVERT: A 145 GLU cc_start: 0.7085 (mp0) cc_final: 0.6750 (mp0) REVERT: A 168 GLU cc_start: 0.7556 (tp30) cc_final: 0.7353 (tp30) REVERT: A 191 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 243 ASP cc_start: 0.8408 (t0) cc_final: 0.7892 (t0) REVERT: A 258 PHE cc_start: 0.6413 (t80) cc_final: 0.6110 (t80) REVERT: A 542 ASN cc_start: 0.8212 (t0) cc_final: 0.7677 (t0) REVERT: B 123 MET cc_start: 0.8367 (ptm) cc_final: 0.8125 (ptt) REVERT: B 168 GLU cc_start: 0.7506 (tp30) cc_final: 0.7300 (tp30) REVERT: B 191 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7511 (tm-30) REVERT: B 243 ASP cc_start: 0.8432 (t0) cc_final: 0.7927 (t0) REVERT: B 258 PHE cc_start: 0.6358 (t80) cc_final: 0.6076 (t80) REVERT: B 542 ASN cc_start: 0.8267 (t0) cc_final: 0.7728 (t0) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3827 time to fit residues: 112.5300 Evaluate side-chains 131 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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: 1.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 348 ASN B 122 GLN B 273 ASN B 348 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9794 Z= 0.190 Angle : 0.562 6.767 13294 Z= 0.301 Chirality : 0.039 0.133 1564 Planarity : 0.004 0.040 1646 Dihedral : 4.727 21.791 1314 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.80 % Favored : 95.04 % Rotamer: Outliers : 1.62 % Allowed : 11.90 % Favored : 86.48 % 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: -1.38 (0.24), residues: 1230 helix: 0.24 (0.19), residues: 720 sheet: -2.01 (0.65), residues: 52 loop : -2.70 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 61 HIS 0.005 0.001 HIS B 359 PHE 0.020 0.001 PHE B 499 TYR 0.017 0.001 TYR A 539 ARG 0.005 0.000 ARG A 316 *********************** 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 166 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.500 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: A 243 ASP cc_start: 0.8468 (t0) cc_final: 0.7933 (t0) REVERT: A 348 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8430 (t0) REVERT: B 123 MET cc_start: 0.8484 (ptm) cc_final: 0.8190 (ptt) REVERT: B 243 ASP cc_start: 0.8525 (t0) cc_final: 0.7986 (t0) REVERT: B 348 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8382 (t0) outliers start: 17 outliers final: 7 residues processed: 157 average time/residue: 0.3436 time to fit residues: 83.8796 Evaluate side-chains 143 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 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: 2.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 348 ASN A 367 GLN B 121 HIS B 367 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 9794 Z= 0.445 Angle : 0.665 6.730 13294 Z= 0.372 Chirality : 0.042 0.157 1564 Planarity : 0.004 0.042 1646 Dihedral : 4.891 20.600 1314 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.53 % Favored : 94.31 % Rotamer: Outliers : 2.48 % Allowed : 17.43 % Favored : 80.10 % 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: -1.00 (0.24), residues: 1230 helix: 0.60 (0.19), residues: 722 sheet: -1.91 (0.71), residues: 38 loop : -2.64 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 61 HIS 0.008 0.002 HIS A 385 PHE 0.023 0.002 PHE A 499 TYR 0.017 0.002 TYR B 539 ARG 0.002 0.000 ARG A 353 *********************** 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 178 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.567 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 revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8613 (ptm) cc_final: 0.8057 (ptt) REVERT: A 243 ASP cc_start: 0.8580 (t0) cc_final: 0.8139 (t0) REVERT: B 243 ASP cc_start: 0.8573 (t0) cc_final: 0.8144 (t0) REVERT: B 362 ASP cc_start: 0.7655 (t0) cc_final: 0.7452 (t0) outliers start: 26 outliers final: 18 residues processed: 160 average time/residue: 0.3132 time to fit residues: 80.6650 Evaluate side-chains 164 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 59 optimal weight: 0.0970 chunk 107 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9794 Z= 0.149 Angle : 0.514 6.436 13294 Z= 0.275 Chirality : 0.039 0.128 1564 Planarity : 0.003 0.033 1646 Dihedral : 4.406 19.851 1314 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 1.33 % Allowed : 19.81 % Favored : 78.86 % 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: -0.25 (0.25), residues: 1230 helix: 1.27 (0.20), residues: 712 sheet: -1.63 (0.70), residues: 52 loop : -2.38 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 456 HIS 0.003 0.001 HIS A 385 PHE 0.017 0.001 PHE A 499 TYR 0.027 0.001 TYR B 276 ARG 0.002 0.000 ARG A 316 *********************** 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 167 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 1.807 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 REVERT: A 53 PHE cc_start: 0.8711 (t80) cc_final: 0.8380 (t80) REVERT: A 123 MET cc_start: 0.8503 (ptm) cc_final: 0.7987 (ptp) REVERT: A 165 MET cc_start: 0.7789 (ttp) cc_final: 0.7585 (ttp) REVERT: A 243 ASP cc_start: 0.8596 (t0) cc_final: 0.8146 (t0) REVERT: B 53 PHE cc_start: 0.8698 (t80) cc_final: 0.8384 (t80) REVERT: B 123 MET cc_start: 0.8629 (ptm) cc_final: 0.7853 (ptp) REVERT: B 243 ASP cc_start: 0.8588 (t0) cc_final: 0.8150 (t0) outliers start: 14 outliers final: 9 residues processed: 162 average time/residue: 0.3227 time to fit residues: 83.3583 Evaluate side-chains 156 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 347 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0570 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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: 0.8075 moved from start: 0.3107 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= 0.229 Angle : 0.537 6.627 13294 Z= 0.289 Chirality : 0.039 0.135 1564 Planarity : 0.003 0.035 1646 Dihedral : 4.324 19.071 1314 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.61 % Favored : 94.23 % Rotamer: Outliers : 2.67 % Allowed : 18.86 % Favored : 78.48 % 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: -0.28 (0.25), residues: 1230 helix: 1.21 (0.19), residues: 726 sheet: -1.57 (0.72), residues: 52 loop : -2.43 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 61 HIS 0.004 0.001 HIS B 385 PHE 0.018 0.001 PHE B 51 TYR 0.030 0.001 TYR A 276 ARG 0.002 0.000 ARG B 353 *********************** 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 175 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 1.624 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 REVERT: A 123 MET cc_start: 0.8721 (ptm) cc_final: 0.8124 (ptp) REVERT: A 165 MET cc_start: 0.7847 (ttp) cc_final: 0.7640 (ttp) REVERT: A 243 ASP cc_start: 0.8603 (t0) cc_final: 0.8159 (t0) REVERT: B 243 ASP cc_start: 0.8607 (t0) cc_final: 0.8171 (t0) outliers start: 28 outliers final: 17 residues processed: 157 average time/residue: 0.3171 time to fit residues: 79.5767 Evaluate side-chains 158 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9794 Z= 0.160 Angle : 0.500 6.539 13294 Z= 0.265 Chirality : 0.039 0.136 1564 Planarity : 0.003 0.032 1646 Dihedral : 4.097 18.442 1314 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 1.81 % Allowed : 20.29 % Favored : 77.90 % 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: 0.05 (0.25), residues: 1230 helix: 1.46 (0.20), residues: 726 sheet: -1.42 (0.73), residues: 52 loop : -2.27 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 466 HIS 0.003 0.001 HIS B 385 PHE 0.019 0.001 PHE B 53 TYR 0.030 0.001 TYR B 276 ARG 0.001 0.000 ARG B 353 *********************** 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 163 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.387 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: A 243 ASP cc_start: 0.8585 (t0) cc_final: 0.8319 (t0) REVERT: B 243 ASP cc_start: 0.8588 (t0) cc_final: 0.8328 (t0) outliers start: 19 outliers final: 11 residues processed: 151 average time/residue: 0.3050 time to fit residues: 73.6088 Evaluate side-chains 148 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 711 SER 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: 4.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8118 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9794 Z= 0.336 Angle : 0.587 6.755 13294 Z= 0.321 Chirality : 0.041 0.151 1564 Planarity : 0.003 0.034 1646 Dihedral : 4.349 18.524 1314 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.07 % Favored : 92.76 % Rotamer: Outliers : 3.05 % Allowed : 19.33 % Favored : 77.62 % 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: -0.32 (0.25), residues: 1230 helix: 1.10 (0.19), residues: 726 sheet: -1.25 (0.78), residues: 46 loop : -2.34 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 61 HIS 0.005 0.001 HIS B 385 PHE 0.021 0.002 PHE A 51 TYR 0.033 0.002 TYR B 276 ARG 0.002 0.000 ARG A 723 *********************** 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 168 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8403 (t80) REVERT: A 243 ASP cc_start: 0.8609 (t0) cc_final: 0.8327 (t0) REVERT: B 123 MET cc_start: 0.8615 (ptm) cc_final: 0.7949 (ptt) REVERT: B 243 ASP cc_start: 0.8615 (t0) cc_final: 0.8338 (t0) REVERT: B 409 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8428 (mt) outliers start: 32 outliers final: 21 residues processed: 148 average time/residue: 0.3266 time to fit residues: 77.4497 Evaluate side-chains 156 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9794 Z= 0.155 Angle : 0.506 6.516 13294 Z= 0.269 Chirality : 0.039 0.156 1564 Planarity : 0.003 0.033 1646 Dihedral : 4.114 18.225 1314 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.28 % Favored : 94.55 % Rotamer: Outliers : 2.29 % Allowed : 20.19 % Favored : 77.52 % 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: 0.07 (0.25), residues: 1230 helix: 1.44 (0.20), residues: 724 sheet: -1.12 (0.77), residues: 46 loop : -2.19 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 61 HIS 0.003 0.001 HIS A 385 PHE 0.020 0.001 PHE B 53 TYR 0.030 0.001 TYR B 276 ARG 0.001 0.000 ARG B 353 *********************** 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 162 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.518 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: A 53 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8377 (t80) REVERT: A 243 ASP cc_start: 0.8559 (t0) cc_final: 0.8269 (t0) REVERT: B 123 MET cc_start: 0.8626 (ptm) cc_final: 0.8389 (ptm) REVERT: B 243 ASP cc_start: 0.8600 (t0) cc_final: 0.8330 (t0) REVERT: B 409 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8479 (mt) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.3184 time to fit residues: 75.8141 Evaluate side-chains 158 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9794 Z= 0.226 Angle : 0.530 6.590 13294 Z= 0.285 Chirality : 0.040 0.185 1564 Planarity : 0.003 0.035 1646 Dihedral : 4.097 18.273 1314 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.50 % Favored : 93.33 % Rotamer: Outliers : 2.19 % Allowed : 20.76 % Favored : 77.05 % 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: 0.06 (0.25), residues: 1230 helix: 1.44 (0.20), residues: 722 sheet: -1.24 (0.76), residues: 46 loop : -2.19 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 61 HIS 0.004 0.001 HIS B 385 PHE 0.020 0.001 PHE A 51 TYR 0.033 0.001 TYR A 276 ARG 0.001 0.000 ARG B 353 *********************** 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 155 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.695 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: A 53 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8442 (t80) REVERT: A 243 ASP cc_start: 0.8576 (t0) cc_final: 0.8290 (t0) REVERT: B 123 MET cc_start: 0.8614 (ptm) cc_final: 0.8332 (ptt) REVERT: B 243 ASP cc_start: 0.8582 (t0) cc_final: 0.8302 (t0) REVERT: B 409 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8493 (mt) outliers start: 23 outliers final: 19 residues processed: 147 average time/residue: 0.3200 time to fit residues: 75.3616 Evaluate side-chains 152 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.8070 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9794 Z= 0.192 Angle : 0.521 6.573 13294 Z= 0.278 Chirality : 0.040 0.210 1564 Planarity : 0.003 0.035 1646 Dihedral : 4.052 18.048 1314 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 1.90 % Allowed : 21.52 % Favored : 76.57 % 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: 0.24 (0.25), residues: 1230 helix: 1.59 (0.20), residues: 718 sheet: -1.22 (0.74), residues: 46 loop : -2.08 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 61 HIS 0.003 0.001 HIS A 385 PHE 0.019 0.001 PHE A 51 TYR 0.032 0.001 TYR B 276 ARG 0.001 0.000 ARG B 353 ********************** 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 157 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.713 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: A 53 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8387 (t80) REVERT: B 243 ASP cc_start: 0.8578 (t0) cc_final: 0.8288 (t0) REVERT: B 409 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8470 (mt) outliers start: 20 outliers final: 17 residues processed: 147 average time/residue: 0.3257 time to fit residues: 77.1309 Evaluate side-chains 152 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 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 = 0.3486 r_free = 0.3486 target = 0.135583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103731 restraints weight = 45432.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.106960 restraints weight = 29916.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.109297 restraints weight = 17331.509| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9794 Z= 0.159 Angle : 0.512 6.978 13294 Z= 0.270 Chirality : 0.039 0.201 1564 Planarity : 0.003 0.034 1646 Dihedral : 3.948 17.762 1314 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.29 % Allowed : 21.62 % Favored : 76.10 % 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: 1.74 (0.20), residues: 716 sheet: -1.13 (0.74), residues: 46 loop : -2.02 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 61 HIS 0.002 0.001 HIS A 385 PHE 0.020 0.001 PHE B 53 TYR 0.031 0.001 TYR A 276 ARG 0.001 0.000 ARG B 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.57 seconds wall clock time: 64 minutes 47.08 seconds (3887.08 seconds total)