Starting phenix.real_space_refine on Sun Nov 17 06:07:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/11_2024/8io7_35610.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/11_2024/8io7_35610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/11_2024/8io7_35610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/11_2024/8io7_35610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/11_2024/8io7_35610.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/11_2024/8io7_35610.cif" } resolution = 2.62 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= 0.004 sd= 0.047 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 8166 2.51 5 N 2194 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12876 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "B" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.93, per 1000 atoms: 0.69 Number of scatterers: 12876 At special positions: 0 Unit cell: (103.75, 103.75, 115.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 4 15.00 Mg 2 11.99 O 2470 8.00 N 2194 7.00 C 8166 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 - 3.00 Amino acid : True - 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 50.9% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.787A pdb=" N GLY A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.682A pdb=" N GLU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.012A pdb=" N PHE A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.503A pdb=" N THR A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.732A pdb=" N LYS A 198 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 200 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 removed outlier: 3.549A pdb=" N ARG A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 255 through 284 removed outlier: 3.513A pdb=" N GLN A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.822A pdb=" N SER A 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.844A pdb=" N LEU A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.120A pdb=" N ILE A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.094A pdb=" N LEU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.863A pdb=" N HIS A 506 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 526 removed outlier: 3.533A pdb=" N GLU A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.778A pdb=" N GLN A 546 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 557 through 564 removed outlier: 3.924A pdb=" N ASN A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 Processing helix chain 'A' and resid 613 through 624 removed outlier: 3.710A pdb=" N LYS A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 664 Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.626A pdb=" N SER A 679 " --> pdb=" O ASP A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 712 through 718 removed outlier: 4.175A pdb=" N VAL A 716 " --> pdb=" O TYR A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.658A pdb=" N ASN A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 770 through 792 removed outlier: 3.625A pdb=" N ASP A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 801 removed outlier: 3.662A pdb=" N TRP A 801 " --> pdb=" O ASP A 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 86 Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.788A pdb=" N GLY B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 removed outlier: 3.682A pdb=" N GLU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.014A pdb=" N PHE B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.504A pdb=" N THR B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 removed outlier: 3.734A pdb=" N LYS B 198 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.549A pdb=" N ARG B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 255 through 284 removed outlier: 3.512A pdb=" N GLN B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.822A pdb=" N SER B 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.843A pdb=" N LEU B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 378 through 383 removed outlier: 4.120A pdb=" N ILE B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 411 through 426 removed outlier: 4.093A pdb=" N LEU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 478 through 492 Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.862A pdb=" N HIS B 506 " --> pdb=" O SER B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 526 removed outlier: 3.534A pdb=" N GLU B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.778A pdb=" N GLN B 546 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 557 through 564 removed outlier: 3.925A pdb=" N ASN B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 613 through 624 removed outlier: 3.709A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 664 Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.627A pdb=" N SER B 679 " --> pdb=" O ASP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 699 Processing helix chain 'B' and resid 712 through 718 removed outlier: 4.175A pdb=" N VAL B 716 " --> pdb=" O TYR B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.658A pdb=" N ASN B 750 " --> pdb=" O MET B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 764 Processing helix chain 'B' and resid 770 through 792 removed outlier: 3.626A pdb=" N ASP B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 800 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.192A pdb=" N ASN A 88 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 92 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLY A 181 " --> pdb=" O ILE A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.192A pdb=" N ASN A 88 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU A 209 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 176 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 211 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA A 178 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS A 213 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 180 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218 removed outlier: 3.901A pdb=" N ASN A 221 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'A' and resid 406 through 410 removed outlier: 6.147A pdb=" N GLY A 407 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR A 610 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 475 removed outlier: 8.766A pdb=" N VAL A 474 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 432 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY A 496 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU A 538 " --> pdb=" O GLY A 496 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP A 498 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER A 540 " --> pdb=" O TRP A 498 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER A 500 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY A 574 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 602 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR A 576 " --> pdb=" O ILE A 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 removed outlier: 5.529A pdb=" N LYS A 452 " --> pdb=" O HIS A 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 625 through 627 removed outlier: 6.248A pdb=" N VAL A 643 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA A 708 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 645 " --> pdb=" O ALA A 708 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.192A pdb=" N ASN B 88 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 92 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLY B 181 " --> pdb=" O ILE B 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.192A pdb=" N ASN B 88 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 174 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU B 209 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 176 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE B 211 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA B 178 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 213 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 180 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 217 through 218 removed outlier: 3.900A pdb=" N ASN B 221 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AB4, first strand: chain 'B' and resid 406 through 410 removed outlier: 6.146A pdb=" N GLY B 407 " --> pdb=" O THR B 610 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N THR B 610 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 475 removed outlier: 8.766A pdb=" N VAL B 474 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 432 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY B 496 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU B 538 " --> pdb=" O GLY B 496 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP B 498 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N SER B 540 " --> pdb=" O TRP B 498 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER B 500 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY B 574 " --> pdb=" O ALA B 600 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE B 602 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B 576 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 452 through 453 removed outlier: 5.529A pdb=" N LYS B 452 " --> pdb=" O HIS B 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 625 through 627 removed outlier: 6.248A pdb=" N VAL B 643 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA B 708 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 645 " --> pdb=" O ALA B 708 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1518 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: 4.51 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2222 1.29 - 1.42: 3573 1.42 - 1.55: 7355 1.55 - 1.68: 10 1.68 - 1.81: 70 Bond restraints: 13230 Sorted by residual: bond pdb=" C GLY B 155 " pdb=" O GLY B 155 " ideal model delta sigma weight residual 1.234 1.160 0.073 1.21e-02 6.83e+03 3.67e+01 bond pdb=" C GLY A 155 " pdb=" O GLY A 155 " ideal model delta sigma weight residual 1.235 1.158 0.077 1.35e-02 5.49e+03 3.26e+01 bond pdb=" O1A TPP A 900 " pdb=" PA TPP A 900 " ideal model delta sigma weight residual 1.479 1.519 -0.040 1.00e-02 1.00e+04 1.61e+01 bond pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 1.516 1.474 0.042 1.09e-02 8.42e+03 1.47e+01 bond pdb=" C GLY A 154 " pdb=" O GLY A 154 " ideal model delta sigma weight residual 1.238 1.184 0.054 1.42e-02 4.96e+03 1.46e+01 ... (remaining 13225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 17480 1.64 - 3.29: 429 3.29 - 4.93: 64 4.93 - 6.57: 23 6.57 - 8.22: 4 Bond angle restraints: 18000 Sorted by residual: angle pdb=" O2B TPP A 900 " pdb=" PB TPP A 900 " pdb=" O3A TPP A 900 " ideal model delta sigma weight residual 104.26 110.74 -6.48 1.33e+00 5.64e-01 2.37e+01 angle pdb=" N GLY B 155 " pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 112.50 107.53 4.97 1.16e+00 7.43e-01 1.83e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 109.40 116.30 -6.90 1.63e+00 3.76e-01 1.79e+01 angle pdb=" N LEU A 157 " pdb=" CA LEU A 157 " pdb=" C LEU A 157 " ideal model delta sigma weight residual 109.40 115.96 -6.56 1.63e+00 3.76e-01 1.62e+01 angle pdb=" O1B TPP A 900 " pdb=" PB TPP A 900 " pdb=" O3A TPP A 900 " ideal model delta sigma weight residual 111.16 104.20 6.96 1.82e+00 3.03e-01 1.47e+01 ... (remaining 17995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 7086 17.69 - 35.39: 521 35.39 - 53.08: 100 53.08 - 70.78: 20 70.78 - 88.47: 17 Dihedral angle restraints: 7744 sinusoidal: 3088 harmonic: 4656 Sorted by residual: dihedral pdb=" CA PHE B 143 " pdb=" C PHE B 143 " pdb=" N ALA B 144 " pdb=" CA ALA B 144 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PHE A 143 " pdb=" C PHE A 143 " pdb=" N ALA A 144 " pdb=" CA ALA A 144 " ideal model delta harmonic sigma weight residual -180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY B 301 " pdb=" C GLY B 301 " pdb=" N TRP B 302 " pdb=" CA TRP B 302 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 7741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1640 0.064 - 0.129: 236 0.129 - 0.193: 10 0.193 - 0.257: 0 0.257 - 0.322: 2 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA LEU A 157 " pdb=" N LEU A 157 " pdb=" C LEU A 157 " pdb=" CB LEU A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA LEU B 157 " pdb=" N LEU B 157 " pdb=" C LEU B 157 " pdb=" CB LEU B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CG LEU B 157 " pdb=" CB LEU B 157 " pdb=" CD1 LEU B 157 " pdb=" CD2 LEU B 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1885 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 156 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" CD GLU B 156 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 156 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 156 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 156 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" CD GLU A 156 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU A 156 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 156 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 558 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C VAL B 558 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 558 " 0.010 2.00e-02 2.50e+03 pdb=" N THR B 559 " 0.009 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 110 2.55 - 3.14: 10560 3.14 - 3.72: 21014 3.72 - 4.31: 30896 4.31 - 4.90: 51245 Nonbonded interactions: 113825 Sorted by model distance: nonbonded pdb=" O2B TPP A 900 " pdb="MG MG A 901 " model vdw 1.959 2.170 nonbonded pdb=" O1B TPP B 900 " pdb="MG MG B 901 " model vdw 1.961 2.170 nonbonded pdb=" OD1 ASN B 215 " pdb="MG MG B 901 " model vdw 2.014 2.170 nonbonded pdb=" OD1 ASN A 215 " pdb="MG MG A 901 " model vdw 2.015 2.170 nonbonded pdb=" O2A TPP B 900 " pdb="MG MG B 901 " model vdw 2.055 2.170 ... (remaining 113820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.120 Find NCS groups from input model: 0.410 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 : 0.005 0.077 13230 Z= 0.364 Angle : 0.657 8.217 18000 Z= 0.393 Chirality : 0.045 0.322 1888 Planarity : 0.004 0.037 2364 Dihedral : 13.653 88.469 4764 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.55 (0.20), residues: 1608 helix: 1.13 (0.20), residues: 648 sheet: -0.09 (0.38), residues: 198 loop : -0.06 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 302 HIS 0.010 0.001 HIS A 320 PHE 0.010 0.001 PHE A 296 TYR 0.009 0.001 TYR B 165 ARG 0.004 0.000 ARG B 717 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.664 Fit side-chains REVERT: A 261 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7463 (mtt-85) REVERT: A 751 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8113 (mtp180) REVERT: B 243 GLU cc_start: 0.8106 (tp30) cc_final: 0.7755 (tp30) REVERT: B 509 ASP cc_start: 0.8503 (m-30) cc_final: 0.8248 (m-30) REVERT: B 688 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7562 (mt-10) outliers start: 0 outliers final: 1 residues processed: 126 average time/residue: 1.5458 time to fit residues: 211.3169 Evaluate side-chains 78 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 382 ILE 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: 4.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13230 Z= 0.339 Angle : 0.578 6.847 18000 Z= 0.312 Chirality : 0.045 0.137 1888 Planarity : 0.004 0.039 2364 Dihedral : 5.792 89.309 1764 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.19 % Allowed : 5.93 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.70 (0.21), residues: 1608 helix: 1.39 (0.20), residues: 656 sheet: -0.27 (0.37), residues: 214 loop : -0.04 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 302 HIS 0.010 0.001 HIS B 320 PHE 0.020 0.002 PHE B 504 TYR 0.013 0.001 TYR A 744 ARG 0.008 0.001 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.583 Fit side-chains REVERT: A 195 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8465 (mm110) REVERT: A 437 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 509 ASP cc_start: 0.8563 (m-30) cc_final: 0.8350 (m-30) REVERT: A 555 ASP cc_start: 0.8291 (t0) cc_final: 0.7835 (t0) REVERT: A 751 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8300 (mtp180) REVERT: B 243 GLU cc_start: 0.8120 (tp30) cc_final: 0.7769 (tp30) REVERT: B 273 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7257 (tp30) REVERT: B 509 ASP cc_start: 0.8625 (m-30) cc_final: 0.8092 (m-30) REVERT: B 555 ASP cc_start: 0.7843 (t0) cc_final: 0.7570 (t0) REVERT: B 618 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7060 (mtm180) outliers start: 16 outliers final: 4 residues processed: 99 average time/residue: 1.4588 time to fit residues: 157.5455 Evaluate side-chains 78 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 775 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 0.0980 chunk 98 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 506 HIS A 714 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 384 ASN B 714 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13230 Z= 0.321 Angle : 0.542 8.955 18000 Z= 0.289 Chirality : 0.044 0.134 1888 Planarity : 0.004 0.042 2364 Dihedral : 5.660 85.894 1762 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.96 % Allowed : 8.00 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.82 (0.21), residues: 1608 helix: 1.53 (0.20), residues: 666 sheet: -0.15 (0.38), residues: 212 loop : -0.06 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 454 HIS 0.008 0.001 HIS B 320 PHE 0.013 0.001 PHE A 504 TYR 0.010 0.001 TYR A 744 ARG 0.008 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.633 Fit side-chains REVERT: A 509 ASP cc_start: 0.8448 (m-30) cc_final: 0.8200 (m-30) REVERT: A 555 ASP cc_start: 0.8298 (t0) cc_final: 0.7912 (t0) REVERT: A 751 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8263 (mtm-85) REVERT: B 243 GLU cc_start: 0.8144 (tp30) cc_final: 0.7784 (tp30) REVERT: B 273 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7318 (tp30) REVERT: B 509 ASP cc_start: 0.8608 (m-30) cc_final: 0.8113 (m-30) REVERT: B 555 ASP cc_start: 0.7814 (t0) cc_final: 0.7375 (t0) REVERT: B 618 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7054 (mtm180) outliers start: 13 outliers final: 4 residues processed: 90 average time/residue: 1.4137 time to fit residues: 139.3894 Evaluate side-chains 79 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 775 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 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 39 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 714 HIS B 39 GLN ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13230 Z= 0.164 Angle : 0.475 6.321 18000 Z= 0.254 Chirality : 0.041 0.127 1888 Planarity : 0.004 0.040 2364 Dihedral : 5.481 84.252 1762 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.33 % Allowed : 8.74 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1608 helix: 1.72 (0.20), residues: 664 sheet: -0.05 (0.38), residues: 212 loop : 0.03 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 454 HIS 0.013 0.001 HIS A 714 PHE 0.010 0.001 PHE B 504 TYR 0.010 0.001 TYR A 744 ARG 0.007 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 195 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8477 (mm110) REVERT: A 509 ASP cc_start: 0.8494 (m-30) cc_final: 0.8216 (m-30) REVERT: A 555 ASP cc_start: 0.8231 (t0) cc_final: 0.7846 (t0) REVERT: A 751 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8296 (mtm-85) REVERT: B 195 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8413 (mm110) REVERT: B 243 GLU cc_start: 0.8122 (tp30) cc_final: 0.7768 (tp30) REVERT: B 273 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7339 (tp30) REVERT: B 436 ASP cc_start: 0.7854 (t0) cc_final: 0.7633 (t0) REVERT: B 509 ASP cc_start: 0.8611 (m-30) cc_final: 0.8051 (m-30) REVERT: B 555 ASP cc_start: 0.7783 (t0) cc_final: 0.7469 (t0) outliers start: 18 outliers final: 5 residues processed: 110 average time/residue: 1.3240 time to fit residues: 161.5510 Evaluate side-chains 94 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 714 HIS 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: 4.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 384 ASN A 714 HIS B 384 ASN B 714 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 13230 Z= 0.500 Angle : 0.593 7.177 18000 Z= 0.315 Chirality : 0.047 0.136 1888 Planarity : 0.004 0.043 2364 Dihedral : 5.684 84.355 1762 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.70 % Allowed : 9.85 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.76 (0.21), residues: 1608 helix: 1.46 (0.20), residues: 664 sheet: -0.12 (0.38), residues: 206 loop : -0.10 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 302 HIS 0.008 0.001 HIS B 714 PHE 0.015 0.002 PHE B 504 TYR 0.012 0.002 TYR B 744 ARG 0.007 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 1.412 Fit side-chains REVERT: A 509 ASP cc_start: 0.8537 (m-30) cc_final: 0.8248 (m-30) REVERT: A 555 ASP cc_start: 0.8250 (t0) cc_final: 0.7936 (t0) REVERT: A 751 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8281 (mtp180) REVERT: A 764 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7674 (mtt) REVERT: B 243 GLU cc_start: 0.8175 (tp30) cc_final: 0.7808 (tp30) REVERT: B 273 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7435 (tp30) REVERT: B 509 ASP cc_start: 0.8662 (m-30) cc_final: 0.8178 (m-30) REVERT: B 555 ASP cc_start: 0.7793 (t0) cc_final: 0.7308 (t0) REVERT: B 618 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7140 (mtm180) outliers start: 23 outliers final: 7 residues processed: 98 average time/residue: 1.3361 time to fit residues: 143.9408 Evaluate side-chains 86 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 618 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13230 Z= 0.172 Angle : 0.490 8.636 18000 Z= 0.258 Chirality : 0.041 0.127 1888 Planarity : 0.004 0.042 2364 Dihedral : 5.447 81.742 1762 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.19 % Allowed : 10.44 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.95 (0.21), residues: 1608 helix: 1.65 (0.20), residues: 668 sheet: -0.20 (0.38), residues: 214 loop : 0.03 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 498 HIS 0.005 0.001 HIS B 77 PHE 0.010 0.001 PHE B 504 TYR 0.011 0.001 TYR A 744 ARG 0.009 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.632 Fit side-chains REVERT: A 195 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8435 (mm110) REVERT: A 481 GLN cc_start: 0.8993 (mm110) cc_final: 0.8262 (mt0) REVERT: A 509 ASP cc_start: 0.8520 (m-30) cc_final: 0.8231 (m-30) REVERT: A 555 ASP cc_start: 0.8192 (t0) cc_final: 0.7864 (t0) REVERT: A 751 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8308 (mtp180) REVERT: A 764 MET cc_start: 0.8051 (mmm) cc_final: 0.7688 (mtt) REVERT: B 195 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8379 (mm110) REVERT: B 243 GLU cc_start: 0.8116 (tp30) cc_final: 0.7790 (tp30) REVERT: B 509 ASP cc_start: 0.8621 (m-30) cc_final: 0.8150 (m-30) REVERT: B 555 ASP cc_start: 0.7763 (t0) cc_final: 0.7374 (t0) outliers start: 16 outliers final: 6 residues processed: 107 average time/residue: 1.2679 time to fit residues: 149.7191 Evaluate side-chains 94 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13230 Z= 0.196 Angle : 0.496 7.415 18000 Z= 0.261 Chirality : 0.041 0.128 1888 Planarity : 0.004 0.042 2364 Dihedral : 5.373 82.145 1762 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.11 % Allowed : 10.81 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1608 helix: 1.73 (0.20), residues: 668 sheet: -0.18 (0.38), residues: 214 loop : 0.09 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 498 HIS 0.005 0.001 HIS A 77 PHE 0.010 0.001 PHE B 504 TYR 0.010 0.001 TYR A 744 ARG 0.009 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.599 Fit side-chains REVERT: A 195 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8405 (mm110) REVERT: A 481 GLN cc_start: 0.8958 (mm110) cc_final: 0.8270 (mt0) REVERT: A 509 ASP cc_start: 0.8526 (m-30) cc_final: 0.8205 (m-30) REVERT: A 555 ASP cc_start: 0.8195 (t0) cc_final: 0.7852 (t0) REVERT: A 751 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8323 (mtp180) REVERT: B 243 GLU cc_start: 0.8135 (tp30) cc_final: 0.7798 (tp30) REVERT: B 509 ASP cc_start: 0.8629 (m-30) cc_final: 0.8359 (m-30) REVERT: B 555 ASP cc_start: 0.7749 (t0) cc_final: 0.7317 (t0) outliers start: 15 outliers final: 11 residues processed: 103 average time/residue: 1.2422 time to fit residues: 141.3324 Evaluate side-chains 96 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13230 Z= 0.215 Angle : 0.495 7.210 18000 Z= 0.261 Chirality : 0.041 0.128 1888 Planarity : 0.004 0.044 2364 Dihedral : 5.362 82.204 1762 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.96 % Allowed : 11.26 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1608 helix: 1.75 (0.20), residues: 668 sheet: -0.17 (0.38), residues: 214 loop : 0.08 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 498 HIS 0.004 0.001 HIS A 77 PHE 0.011 0.001 PHE B 504 TYR 0.016 0.001 TYR A 489 ARG 0.009 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.418 Fit side-chains REVERT: A 481 GLN cc_start: 0.8947 (mm110) cc_final: 0.8286 (mt0) REVERT: A 509 ASP cc_start: 0.8536 (m-30) cc_final: 0.8213 (m-30) REVERT: A 555 ASP cc_start: 0.8195 (t0) cc_final: 0.7844 (t0) REVERT: A 751 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8320 (mtp180) REVERT: B 243 GLU cc_start: 0.8151 (tp30) cc_final: 0.7818 (tp30) REVERT: B 509 ASP cc_start: 0.8637 (m-30) cc_final: 0.8352 (m-30) REVERT: B 555 ASP cc_start: 0.7698 (t0) cc_final: 0.7282 (t0) outliers start: 13 outliers final: 11 residues processed: 98 average time/residue: 1.2476 time to fit residues: 135.1726 Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 0.0670 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13230 Z= 0.177 Angle : 0.492 6.977 18000 Z= 0.258 Chirality : 0.041 0.126 1888 Planarity : 0.004 0.043 2364 Dihedral : 5.293 82.239 1762 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.04 % Allowed : 11.41 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1608 helix: 1.82 (0.20), residues: 668 sheet: -0.19 (0.38), residues: 214 loop : 0.12 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 498 HIS 0.005 0.001 HIS A 77 PHE 0.010 0.001 PHE B 504 TYR 0.011 0.001 TYR A 489 ARG 0.010 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.648 Fit side-chains REVERT: A 481 GLN cc_start: 0.8916 (mm110) cc_final: 0.8302 (mt0) REVERT: A 509 ASP cc_start: 0.8527 (m-30) cc_final: 0.8185 (m-30) REVERT: A 555 ASP cc_start: 0.8161 (t0) cc_final: 0.7810 (t0) REVERT: A 751 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.8325 (mtp180) REVERT: B 243 GLU cc_start: 0.8139 (tp30) cc_final: 0.7809 (tp30) REVERT: B 509 ASP cc_start: 0.8624 (m-30) cc_final: 0.8339 (m-30) REVERT: B 555 ASP cc_start: 0.7679 (t0) cc_final: 0.7248 (t0) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 1.1773 time to fit residues: 137.8275 Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13230 Z= 0.186 Angle : 0.508 6.992 18000 Z= 0.267 Chirality : 0.041 0.155 1888 Planarity : 0.004 0.043 2364 Dihedral : 5.281 82.199 1762 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.89 % Allowed : 12.07 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1608 helix: 1.76 (0.20), residues: 672 sheet: -0.13 (0.38), residues: 202 loop : 0.09 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 498 HIS 0.004 0.001 HIS A 77 PHE 0.010 0.001 PHE B 504 TYR 0.011 0.001 TYR A 489 ARG 0.010 0.000 ARG A 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.513 Fit side-chains REVERT: A 481 GLN cc_start: 0.8898 (mm110) cc_final: 0.8326 (mt0) REVERT: A 509 ASP cc_start: 0.8532 (m-30) cc_final: 0.8189 (m-30) REVERT: A 555 ASP cc_start: 0.8156 (t0) cc_final: 0.7804 (t0) REVERT: A 751 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8329 (mtp180) REVERT: B 243 GLU cc_start: 0.8147 (tp30) cc_final: 0.7800 (tp30) REVERT: B 509 ASP cc_start: 0.8629 (m-30) cc_final: 0.8343 (m-30) REVERT: B 555 ASP cc_start: 0.7661 (t0) cc_final: 0.7258 (t0) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 1.1648 time to fit residues: 128.1589 Evaluate side-chains 94 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 714 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 384 ASN B 714 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.070950 restraints weight = 26081.186| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.70 r_work: 0.2890 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13230 Z= 0.232 Angle : 0.518 6.738 18000 Z= 0.273 Chirality : 0.042 0.174 1888 Planarity : 0.004 0.043 2364 Dihedral : 5.293 82.164 1762 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.89 % Allowed : 12.22 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1608 helix: 1.74 (0.20), residues: 672 sheet: -0.13 (0.38), residues: 202 loop : 0.07 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 498 HIS 0.004 0.001 HIS A 77 PHE 0.011 0.001 PHE B 504 TYR 0.009 0.001 TYR A 744 ARG 0.009 0.000 ARG A 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3603.53 seconds wall clock time: 66 minutes 11.46 seconds (3971.46 seconds total)