Starting phenix.real_space_refine on Fri Mar 15 18:31:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/03_2024/8dtf_27696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/03_2024/8dtf_27696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/03_2024/8dtf_27696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/03_2024/8dtf_27696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/03_2024/8dtf_27696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/03_2024/8dtf_27696.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 7907 2.51 5 N 2071 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 550": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12414 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6203 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 767} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 6211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6211 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 767} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 6.79, per 1000 atoms: 0.55 Number of scatterers: 12414 At special positions: 0 Unit cell: (164.56, 106.48, 97.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2340 8.00 N 2071 7.00 C 7907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.22 Conformation dependent library (CDL) restraints added in 2.1 seconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3032 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 4 sheets defined 72.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 58 through 73 removed outlier: 3.535A pdb=" N LYS A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.684A pdb=" N GLU A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 removed outlier: 3.579A pdb=" N ALA A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 185 through 199 removed outlier: 3.640A pdb=" N TYR A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.511A pdb=" N TYR A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 250 removed outlier: 4.016A pdb=" N ALA A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 275 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.529A pdb=" N TYR A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 310 through 325 Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 430 through 445 removed outlier: 3.693A pdb=" N TYR A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 497 through 507 removed outlier: 5.067A pdb=" N ALA A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.611A pdb=" N LYS A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 576 through 582 Processing helix chain 'A' and resid 647 through 653 removed outlier: 3.984A pdb=" N SER A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 667 through 681 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 695 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 732 through 735 removed outlier: 3.528A pdb=" N MET A 735 " --> pdb=" O TYR A 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 732 through 735' Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 767 through 781 removed outlier: 5.008A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.585A pdb=" N ASP A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 821 removed outlier: 4.697A pdb=" N ARG A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 816 " --> pdb=" O MET A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 824 No H-bonds generated for 'chain 'A' and resid 822 through 824' Processing helix chain 'A' and resid 825 through 846 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 73 removed outlier: 3.536A pdb=" N LYS B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 92 through 107 Processing helix chain 'B' and resid 110 through 124 removed outlier: 3.684A pdb=" N GLU B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 141 removed outlier: 3.580A pdb=" N ALA B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 165 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.640A pdb=" N TYR B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.510A pdb=" N TYR B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 250 removed outlier: 4.016A pdb=" N ALA B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 275 Processing helix chain 'B' and resid 276 through 291 removed outlier: 3.529A pdb=" N TYR B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 309 Processing helix chain 'B' and resid 310 through 325 Processing helix chain 'B' and resid 328 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 396 through 410 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.693A pdb=" N TYR B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 466 Processing helix chain 'B' and resid 497 through 507 removed outlier: 5.067A pdb=" N ALA B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Proline residue: B 504 - end of helix Processing helix chain 'B' and resid 525 through 539 removed outlier: 3.611A pdb=" N LYS B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 560 Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 647 through 653 removed outlier: 3.983A pdb=" N SER B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 667 through 681 Processing helix chain 'B' and resid 691 through 694 Processing helix chain 'B' and resid 695 through 709 Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 732 through 735 removed outlier: 3.528A pdb=" N MET B 735 " --> pdb=" O TYR B 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 732 through 735' Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 767 through 781 removed outlier: 5.010A pdb=" N GLY B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 774 " --> pdb=" O HIS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 789 through 803 removed outlier: 3.585A pdb=" N ASP B 803 " --> pdb=" O ASP B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 removed outlier: 4.697A pdb=" N ARG B 815 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP B 816 " --> pdb=" O MET B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 824 No H-bonds generated for 'chain 'B' and resid 822 through 824' Processing helix chain 'B' and resid 825 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 544 removed outlier: 8.168A pdb=" N VAL A 541 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 515 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LYS A 543 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL A 517 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 483 " --> pdb=" O LYS A 514 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL A 516 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 485 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TYR A 518 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR A 487 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN A 588 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 607 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A 590 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N ASP A 609 " --> pdb=" O THR A 590 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG A 606 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 628 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR A 608 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 719 removed outlier: 8.654A pdb=" N ASP A 717 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 686 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU A 719 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 688 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER A 738 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N MET A 763 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA A 787 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 762 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 541 through 544 removed outlier: 8.167A pdb=" N VAL B 541 " --> pdb=" O TYR B 513 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 515 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LYS B 543 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL B 517 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 483 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL B 516 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE B 485 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TYR B 518 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR B 487 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR B 484 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL B 566 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 486 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN B 588 " --> pdb=" O TYR B 605 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE B 607 " --> pdb=" O GLN B 588 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR B 590 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N ASP B 609 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 606 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU B 628 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR B 608 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 716 through 719 removed outlier: 8.652A pdb=" N ASP B 717 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 686 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU B 719 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 688 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER B 738 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N MET B 763 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA B 787 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR B 762 " --> pdb=" O ALA B 787 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2412 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: 4.30 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4041 1.34 - 1.46: 1950 1.46 - 1.58: 6565 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 12698 Sorted by residual: bond pdb=" CG LEU B 628 " pdb=" CD1 LEU B 628 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CG LEU A 628 " pdb=" CD1 LEU A 628 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CB ILE A 607 " pdb=" CG2 ILE A 607 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.12e+00 bond pdb=" CB ILE B 607 " pdb=" CG2 ILE B 607 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.12e+00 bond pdb=" CE LYS B 174 " pdb=" NZ LYS B 174 " ideal model delta sigma weight residual 1.489 1.453 0.036 3.00e-02 1.11e+03 1.47e+00 ... (remaining 12693 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.14: 274 105.14 - 112.44: 6191 112.44 - 119.74: 4701 119.74 - 127.04: 5977 127.04 - 134.34: 142 Bond angle restraints: 17285 Sorted by residual: angle pdb=" C THR B 590 " pdb=" N TRP B 591 " pdb=" CA TRP B 591 " ideal model delta sigma weight residual 121.54 115.33 6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C THR A 590 " pdb=" N TRP A 591 " pdb=" CA TRP A 591 " ideal model delta sigma weight residual 121.54 115.35 6.19 1.91e+00 2.74e-01 1.05e+01 angle pdb=" CA GLU A 170 " pdb=" CB GLU A 170 " pdb=" CG GLU A 170 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.07e+00 angle pdb=" CA GLU B 170 " pdb=" CB GLU B 170 " pdb=" CG GLU B 170 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.89e+00 angle pdb=" N ILE A 592 " pdb=" CA ILE A 592 " pdb=" C ILE A 592 " ideal model delta sigma weight residual 109.34 115.51 -6.17 2.08e+00 2.31e-01 8.80e+00 ... (remaining 17280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 7054 17.10 - 34.21: 421 34.21 - 51.31: 90 51.31 - 68.42: 14 68.42 - 85.52: 6 Dihedral angle restraints: 7585 sinusoidal: 2853 harmonic: 4732 Sorted by residual: dihedral pdb=" CA ALA B 745 " pdb=" C ALA B 745 " pdb=" N GLY B 746 " pdb=" CA GLY B 746 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ALA A 745 " pdb=" C ALA A 745 " pdb=" N GLY A 746 " pdb=" CA GLY A 746 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR A 656 " pdb=" C THR A 656 " pdb=" N PHE A 657 " pdb=" CA PHE A 657 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 7582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1451 0.043 - 0.087: 355 0.087 - 0.130: 113 0.130 - 0.174: 19 0.174 - 0.217: 6 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CA GLU B 170 " pdb=" N GLU B 170 " pdb=" C GLU B 170 " pdb=" CB GLU B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU A 170 " pdb=" N GLU A 170 " pdb=" C GLU A 170 " pdb=" CB GLU A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA PHE B 463 " pdb=" N PHE B 463 " pdb=" C PHE B 463 " pdb=" CB PHE B 463 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 1941 not shown) Planarity restraints: 2231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 463 " 0.028 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE B 463 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 463 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 463 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 463 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 463 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 463 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 463 " -0.028 2.00e-02 2.50e+03 2.07e-02 7.52e+00 pdb=" CG PHE A 463 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 463 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 463 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 463 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 463 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 463 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 393 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 394 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " 0.031 5.00e-02 4.00e+02 ... (remaining 2228 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2549 2.78 - 3.31: 13295 3.31 - 3.84: 21903 3.84 - 4.37: 25730 4.37 - 4.90: 42378 Nonbonded interactions: 105855 Sorted by model distance: nonbonded pdb=" O LYS A 58 " pdb=" OD1 ASP A 61 " model vdw 2.250 3.040 nonbonded pdb=" O LYS B 58 " pdb=" OD1 ASP B 61 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 484 " pdb=" O LYS A 561 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR B 484 " pdb=" O LYS B 561 " model vdw 2.266 2.440 nonbonded pdb=" OD1 ASN B 442 " pdb=" OH TYR B 594 " model vdw 2.322 2.440 ... (remaining 105850 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' and (resid 44 through 511 or (resid 512 and (name N or name CA or nam \ e C or name O or name CB )) or resid 513 through 558 or (resid 559 and (name N o \ r name CA or name C or name O or name CB )) or resid 560 through 846)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.190 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 36.050 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12698 Z= 0.209 Angle : 0.722 8.406 17285 Z= 0.401 Chirality : 0.044 0.217 1944 Planarity : 0.006 0.056 2231 Dihedral : 11.936 85.520 4553 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.20), residues: 1602 helix: 0.78 (0.14), residues: 1100 sheet: 0.72 (0.54), residues: 102 loop : -1.27 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 459 HIS 0.004 0.001 HIS B 508 PHE 0.046 0.003 PHE B 463 TYR 0.038 0.004 TYR B 284 ARG 0.013 0.002 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8145 (mp) cc_final: 0.7880 (tt) REVERT: B 452 LEU cc_start: 0.8446 (tp) cc_final: 0.8239 (tp) REVERT: B 466 LEU cc_start: 0.8127 (mp) cc_final: 0.7877 (tt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1884 time to fit residues: 49.6928 Evaluate side-chains 122 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 167 ASN A 619 GLN B 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12698 Z= 0.217 Angle : 0.570 6.540 17285 Z= 0.293 Chirality : 0.041 0.238 1944 Planarity : 0.004 0.040 2231 Dihedral : 3.849 15.932 1756 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.68 % Allowed : 5.97 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.21), residues: 1602 helix: 2.02 (0.15), residues: 1104 sheet: 0.58 (0.52), residues: 104 loop : -0.25 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 459 HIS 0.005 0.001 HIS A 293 PHE 0.017 0.002 PHE A 253 TYR 0.022 0.002 TYR A 284 ARG 0.004 0.001 ARG B 676 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 756 MET cc_start: 0.7511 (mmm) cc_final: 0.7236 (mmt) outliers start: 22 outliers final: 14 residues processed: 126 average time/residue: 0.1948 time to fit residues: 39.0336 Evaluate side-chains 122 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 461 TRP Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 0.0270 chunk 129 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12698 Z= 0.279 Angle : 0.583 10.649 17285 Z= 0.292 Chirality : 0.041 0.156 1944 Planarity : 0.004 0.038 2231 Dihedral : 3.880 16.162 1756 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 7.58 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.21), residues: 1602 helix: 2.27 (0.15), residues: 1110 sheet: 0.50 (0.54), residues: 108 loop : -0.42 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 292 HIS 0.003 0.001 HIS B 495 PHE 0.019 0.002 PHE A 253 TYR 0.020 0.002 TYR A 732 ARG 0.006 0.001 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7258 (m100) cc_final: 0.6959 (m100) outliers start: 26 outliers final: 16 residues processed: 149 average time/residue: 0.1908 time to fit residues: 45.0896 Evaluate side-chains 129 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12698 Z= 0.190 Angle : 0.519 9.006 17285 Z= 0.258 Chirality : 0.039 0.134 1944 Planarity : 0.004 0.037 2231 Dihedral : 3.844 15.505 1756 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.68 % Allowed : 9.88 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.22), residues: 1602 helix: 2.47 (0.16), residues: 1110 sheet: 0.51 (0.55), residues: 108 loop : -0.41 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 841 HIS 0.002 0.001 HIS A 768 PHE 0.018 0.001 PHE B 829 TYR 0.026 0.001 TYR A 732 ARG 0.003 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7254 (m100) cc_final: 0.6930 (m100) REVERT: A 633 LEU cc_start: 0.8812 (mt) cc_final: 0.8515 (mt) REVERT: B 134 TYR cc_start: 0.6638 (m-80) cc_final: 0.6289 (m-80) REVERT: B 461 TRP cc_start: 0.7237 (m100) cc_final: 0.6914 (m100) REVERT: B 633 LEU cc_start: 0.8843 (mt) cc_final: 0.8542 (mt) outliers start: 22 outliers final: 17 residues processed: 136 average time/residue: 0.1908 time to fit residues: 41.0142 Evaluate side-chains 128 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 115 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12698 Z= 0.305 Angle : 0.571 7.943 17285 Z= 0.286 Chirality : 0.041 0.173 1944 Planarity : 0.004 0.037 2231 Dihedral : 3.931 16.722 1756 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.91 % Allowed : 10.80 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.22), residues: 1602 helix: 2.38 (0.15), residues: 1112 sheet: 0.36 (0.59), residues: 96 loop : -0.70 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 841 HIS 0.017 0.001 HIS A 508 PHE 0.021 0.002 PHE A 654 TYR 0.020 0.001 TYR A 134 ARG 0.003 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7255 (m100) cc_final: 0.6948 (m100) REVERT: A 633 LEU cc_start: 0.8998 (mt) cc_final: 0.8773 (mt) REVERT: A 800 LEU cc_start: 0.8534 (tp) cc_final: 0.8196 (tt) REVERT: B 633 LEU cc_start: 0.9008 (mt) cc_final: 0.8779 (mt) REVERT: B 654 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.5806 (t80) REVERT: B 800 LEU cc_start: 0.8544 (tp) cc_final: 0.8212 (tt) outliers start: 25 outliers final: 20 residues processed: 130 average time/residue: 0.2126 time to fit residues: 42.7797 Evaluate side-chains 130 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 154 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12698 Z= 0.184 Angle : 0.516 8.568 17285 Z= 0.255 Chirality : 0.039 0.206 1944 Planarity : 0.004 0.037 2231 Dihedral : 3.867 16.709 1756 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.76 % Allowed : 10.95 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.22), residues: 1602 helix: 2.55 (0.16), residues: 1112 sheet: 0.36 (0.59), residues: 96 loop : -0.71 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 841 HIS 0.003 0.001 HIS A 293 PHE 0.015 0.001 PHE B 654 TYR 0.024 0.001 TYR A 732 ARG 0.004 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7222 (m100) cc_final: 0.6936 (m100) REVERT: A 546 TYR cc_start: 0.7710 (t80) cc_final: 0.7496 (t80) REVERT: A 564 ILE cc_start: 0.6530 (mt) cc_final: 0.6283 (mt) REVERT: A 633 LEU cc_start: 0.8963 (mt) cc_final: 0.8743 (mt) REVERT: A 654 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5928 (t80) REVERT: B 461 TRP cc_start: 0.7227 (m100) cc_final: 0.6900 (m100) REVERT: B 633 LEU cc_start: 0.8997 (mt) cc_final: 0.8768 (mt) outliers start: 23 outliers final: 18 residues processed: 135 average time/residue: 0.2048 time to fit residues: 43.0349 Evaluate side-chains 129 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 GLN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12698 Z= 0.261 Angle : 0.551 8.157 17285 Z= 0.272 Chirality : 0.039 0.148 1944 Planarity : 0.004 0.037 2231 Dihedral : 3.858 16.762 1756 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.07 % Allowed : 11.33 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.22), residues: 1602 helix: 2.52 (0.16), residues: 1112 sheet: 0.35 (0.60), residues: 96 loop : -0.83 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 841 HIS 0.007 0.001 HIS A 508 PHE 0.012 0.001 PHE B 829 TYR 0.023 0.001 TYR A 732 ARG 0.003 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ILE cc_start: 0.6558 (mt) cc_final: 0.6296 (mt) REVERT: A 633 LEU cc_start: 0.8982 (mt) cc_final: 0.8772 (mt) REVERT: A 654 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6073 (t80) REVERT: A 756 MET cc_start: 0.7616 (mmm) cc_final: 0.7302 (mmt) REVERT: A 800 LEU cc_start: 0.8527 (tp) cc_final: 0.8225 (tt) REVERT: B 461 TRP cc_start: 0.7269 (m100) cc_final: 0.6964 (m100) REVERT: B 633 LEU cc_start: 0.9030 (mt) cc_final: 0.8804 (mt) REVERT: B 654 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.5965 (t80) outliers start: 27 outliers final: 20 residues processed: 137 average time/residue: 0.2175 time to fit residues: 46.1486 Evaluate side-chains 131 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12698 Z= 0.171 Angle : 0.524 7.345 17285 Z= 0.259 Chirality : 0.038 0.137 1944 Planarity : 0.004 0.038 2231 Dihedral : 3.826 16.481 1756 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.45 % Allowed : 12.40 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.22), residues: 1602 helix: 2.61 (0.16), residues: 1110 sheet: 0.41 (0.61), residues: 96 loop : -0.75 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 841 HIS 0.004 0.001 HIS A 508 PHE 0.011 0.001 PHE B 654 TYR 0.024 0.001 TYR A 732 ARG 0.003 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7270 (m100) cc_final: 0.6951 (m100) REVERT: A 654 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6101 (t80) REVERT: A 800 LEU cc_start: 0.8550 (tp) cc_final: 0.8266 (tt) REVERT: B 461 TRP cc_start: 0.7208 (m100) cc_final: 0.6917 (m100) REVERT: B 633 LEU cc_start: 0.8989 (mt) cc_final: 0.8777 (mt) REVERT: B 654 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.6099 (t80) outliers start: 19 outliers final: 15 residues processed: 132 average time/residue: 0.2041 time to fit residues: 42.4117 Evaluate side-chains 124 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12698 Z= 0.172 Angle : 0.536 9.697 17285 Z= 0.263 Chirality : 0.039 0.155 1944 Planarity : 0.004 0.038 2231 Dihedral : 3.782 18.667 1756 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.45 % Allowed : 13.02 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.22), residues: 1602 helix: 2.59 (0.16), residues: 1114 sheet: 0.35 (0.61), residues: 96 loop : -0.80 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 841 HIS 0.004 0.001 HIS A 508 PHE 0.011 0.001 PHE B 654 TYR 0.023 0.001 TYR A 732 ARG 0.002 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ILE cc_start: 0.6532 (mt) cc_final: 0.6288 (mt) REVERT: A 654 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.6198 (t80) REVERT: A 800 LEU cc_start: 0.8597 (tp) cc_final: 0.8303 (tt) REVERT: B 633 LEU cc_start: 0.8991 (mt) cc_final: 0.8754 (mt) REVERT: B 654 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6030 (t80) outliers start: 19 outliers final: 14 residues processed: 125 average time/residue: 0.2044 time to fit residues: 39.7329 Evaluate side-chains 124 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 0.0970 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 13 optimal weight: 0.0770 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN A 442 ASN A 508 HIS ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12698 Z= 0.170 Angle : 0.533 9.815 17285 Z= 0.262 Chirality : 0.038 0.151 1944 Planarity : 0.004 0.038 2231 Dihedral : 3.785 18.564 1756 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.30 % Allowed : 13.48 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.22), residues: 1602 helix: 2.59 (0.16), residues: 1116 sheet: 0.29 (0.61), residues: 96 loop : -0.79 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 841 HIS 0.013 0.001 HIS A 508 PHE 0.011 0.001 PHE B 654 TYR 0.027 0.001 TYR A 732 ARG 0.002 0.000 ARG B 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ILE cc_start: 0.6485 (mt) cc_final: 0.6242 (mt) REVERT: A 569 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8735 (p) REVERT: A 654 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6181 (t80) REVERT: A 800 LEU cc_start: 0.8597 (tp) cc_final: 0.8334 (tt) REVERT: B 633 LEU cc_start: 0.9014 (mt) cc_final: 0.8761 (mt) REVERT: B 654 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.6073 (t80) outliers start: 17 outliers final: 13 residues processed: 127 average time/residue: 0.1998 time to fit residues: 39.5694 Evaluate side-chains 126 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.4980 chunk 38 optimal weight: 0.0870 chunk 117 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.0270 chunk 127 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 402 ASN A 571 HIS B 442 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.127531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088668 restraints weight = 28571.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.089077 restraints weight = 17035.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089333 restraints weight = 12782.467| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12698 Z= 0.148 Angle : 0.524 9.639 17285 Z= 0.256 Chirality : 0.038 0.152 1944 Planarity : 0.004 0.039 2231 Dihedral : 3.745 18.433 1756 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.23 % Allowed : 13.48 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.22), residues: 1602 helix: 2.68 (0.16), residues: 1112 sheet: 0.17 (0.56), residues: 108 loop : -0.72 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 841 HIS 0.003 0.001 HIS B 768 PHE 0.011 0.001 PHE B 654 TYR 0.024 0.001 TYR A 732 ARG 0.003 0.000 ARG B 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.20 seconds wall clock time: 41 minutes 25.87 seconds (2485.87 seconds total)