Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 15:24:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/07_2023/8dtf_27696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/07_2023/8dtf_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_27696/07_2023/8dtf_27696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/07_2023/8dtf_27696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/07_2023/8dtf_27696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtf_27696/07_2023/8dtf_27696.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-1.21rc1-5013/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: 6.24, per 1000 atoms: 0.50 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: 5.05 Conformation dependent library (CDL) restraints added in 1.7 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: 0.77 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: 4.58 Time building geometry restraints manager: 5.42 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: 2.740 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: 12.770 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 33.770 Find NCS groups from input model: 0.690 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.150 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2016 time to fit residues: 52.6947 Evaluate side-chains 120 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9091 ------------------------------------------------------------------------------- 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: 2.9990 chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 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: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 619 GLN B 167 ASN B 619 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12698 Z= 0.210 Angle : 0.582 10.336 17285 Z= 0.294 Chirality : 0.042 0.275 1944 Planarity : 0.004 0.039 2231 Dihedral : 3.867 16.164 1756 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer Outliers : 1.53 % 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: 2.09 (0.22), residues: 1602 helix: 2.05 (0.15), residues: 1104 sheet: 0.57 (0.52), residues: 104 loop : -0.24 (0.34), residues: 394 *********************** 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 136 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 128 average time/residue: 0.1966 time to fit residues: 40.4884 Evaluate side-chains 119 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1185 time to fit residues: 4.2943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 12698 Z= 0.313 Angle : 0.596 8.258 17285 Z= 0.302 Chirality : 0.041 0.126 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.917 16.465 1756 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.15 % 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: 2.17 (0.21), residues: 1602 helix: 2.18 (0.15), residues: 1108 sheet: 0.44 (0.53), residues: 108 loop : -0.46 (0.34), residues: 386 *********************** 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 141 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 137 average time/residue: 0.2026 time to fit residues: 43.7652 Evaluate side-chains 119 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1189 time to fit residues: 3.4100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 508 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 12698 Z= 0.292 Angle : 0.566 7.326 17285 Z= 0.284 Chirality : 0.040 0.133 1944 Planarity : 0.004 0.046 2231 Dihedral : 3.974 16.297 1756 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.07 % 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: 2.21 (0.21), residues: 1602 helix: 2.30 (0.15), residues: 1108 sheet: 0.45 (0.59), residues: 96 loop : -0.70 (0.32), residues: 398 *********************** 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 134 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 0.2069 time to fit residues: 42.6501 Evaluate side-chains 113 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1818 time to fit residues: 4.4695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 0.0030 chunk 63 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 0.0570 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 12698 Z= 0.153 Angle : 0.519 8.456 17285 Z= 0.255 Chirality : 0.039 0.201 1944 Planarity : 0.004 0.045 2231 Dihedral : 3.891 16.169 1756 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.69 % 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: 2.49 (0.22), residues: 1602 helix: 2.51 (0.16), residues: 1112 sheet: 0.39 (0.59), residues: 96 loop : -0.58 (0.32), residues: 394 *********************** 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 121 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 118 average time/residue: 0.2117 time to fit residues: 39.4107 Evaluate side-chains 102 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1485 time to fit residues: 2.0135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN B 402 ASN ** B 575 ASN ** 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: 0.7999 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12698 Z= 0.204 Angle : 0.533 10.688 17285 Z= 0.261 Chirality : 0.039 0.148 1944 Planarity : 0.004 0.044 2231 Dihedral : 3.876 16.354 1756 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.54 % 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: 2.46 (0.22), residues: 1602 helix: 2.53 (0.16), residues: 1114 sheet: 0.35 (0.60), residues: 96 loop : -0.74 (0.32), residues: 392 *********************** 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 110 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.2146 time to fit residues: 36.5556 Evaluate side-chains 103 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1215 time to fit residues: 3.1476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 GLN B 367 ASN B 402 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12698 Z= 0.272 Angle : 0.558 8.671 17285 Z= 0.279 Chirality : 0.040 0.165 1944 Planarity : 0.004 0.044 2231 Dihedral : 3.963 18.609 1756 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.54 % 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: 2.32 (0.22), residues: 1602 helix: 2.47 (0.15), residues: 1114 sheet: 0.21 (0.60), residues: 96 loop : -0.93 (0.31), residues: 392 *********************** 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 116 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 112 average time/residue: 0.2066 time to fit residues: 36.6167 Evaluate side-chains 101 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1076 time to fit residues: 2.0175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12698 Z= 0.177 Angle : 0.520 8.493 17285 Z= 0.257 Chirality : 0.038 0.134 1944 Planarity : 0.004 0.044 2231 Dihedral : 3.888 18.316 1756 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.46 % 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: 2.43 (0.22), residues: 1602 helix: 2.56 (0.16), residues: 1114 sheet: 0.17 (0.60), residues: 96 loop : -0.91 (0.31), residues: 392 *********************** 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 115 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 112 average time/residue: 0.2163 time to fit residues: 38.7089 Evaluate side-chains 101 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1351 time to fit residues: 2.5315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 0.0000 chunk 143 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 0.0570 chunk 112 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 overall best weight: 0.2702 ------------------------------------------------------------------------------- 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN B 402 ASN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 12698 Z= 0.141 Angle : 0.519 9.102 17285 Z= 0.254 Chirality : 0.038 0.152 1944 Planarity : 0.004 0.046 2231 Dihedral : 3.827 17.827 1756 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.38 % 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: 2.56 (0.22), residues: 1602 helix: 2.65 (0.16), residues: 1116 sheet: 0.18 (0.61), residues: 96 loop : -0.82 (0.32), residues: 390 *********************** 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 117 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 115 average time/residue: 0.2115 time to fit residues: 39.0541 Evaluate side-chains 106 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1190 time to fit residues: 2.4015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 159 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 B 442 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12698 Z= 0.178 Angle : 0.543 13.323 17285 Z= 0.264 Chirality : 0.039 0.157 1944 Planarity : 0.004 0.045 2231 Dihedral : 3.802 18.029 1756 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.08 % 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: 2.58 (0.22), residues: 1602 helix: 2.66 (0.16), residues: 1116 sheet: 0.29 (0.62), residues: 94 loop : -0.84 (0.32), residues: 392 ********************** 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 106 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.2074 time to fit residues: 35.3706 Evaluate side-chains 102 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1227 time to fit residues: 2.4622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN A 571 HIS B 442 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.127280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088856 restraints weight = 28481.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089257 restraints weight = 15948.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089071 restraints weight = 13194.880| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 12698 Z= 0.161 Angle : 0.540 12.074 17285 Z= 0.260 Chirality : 0.039 0.152 1944 Planarity : 0.004 0.046 2231 Dihedral : 3.770 17.816 1756 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.23 % 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: 2.66 (0.22), residues: 1602 helix: 2.71 (0.16), residues: 1112 sheet: 0.37 (0.62), residues: 94 loop : -0.74 (0.32), residues: 396 =============================================================================== Job complete usr+sys time: 2107.67 seconds wall clock time: 40 minutes 0.54 seconds (2400.54 seconds total)