Starting phenix.real_space_refine on Tue Apr 9 07:35:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttr_26121/04_2024/7ttr_26121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttr_26121/04_2024/7ttr_26121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttr_26121/04_2024/7ttr_26121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttr_26121/04_2024/7ttr_26121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttr_26121/04_2024/7ttr_26121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttr_26121/04_2024/7ttr_26121_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.070 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 14 5.49 5 Mg 4 5.21 5 S 54 5.16 5 C 9890 2.51 5 N 2841 2.21 5 O 2894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B ARG 546": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 590": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ARG 620": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B ARG 650": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 417": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C ARG 546": "NH1" <-> "NH2" Residue "C ARG 554": "NH1" <-> "NH2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C ARG 561": "NH1" <-> "NH2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "C ARG 620": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 629": "NH1" <-> "NH2" Residue "C ARG 650": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 408": "NH1" <-> "NH2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D ARG 546": "NH1" <-> "NH2" Residue "D ARG 554": "NH1" <-> "NH2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "D ARG 561": "NH1" <-> "NH2" Residue "D ARG 590": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D ARG 620": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 629": "NH1" <-> "NH2" Residue "D ARG 650": "NH1" <-> "NH2" Residue "D ARG 674": "NH1" <-> "NH2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 334": "NH1" <-> "NH2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E ARG 362": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 408": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E ARG 475": "NH1" <-> "NH2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E ARG 546": "NH1" <-> "NH2" Residue "E ARG 554": "NH1" <-> "NH2" Residue "E ARG 555": "NH1" <-> "NH2" Residue "E ARG 561": "NH1" <-> "NH2" Residue "E ARG 590": "NH1" <-> "NH2" Residue "E ARG 594": "NH1" <-> "NH2" Residue "E ARG 603": "NH1" <-> "NH2" Residue "E ARG 620": "NH1" <-> "NH2" Residue "E ARG 628": "NH1" <-> "NH2" Residue "E ARG 629": "NH1" <-> "NH2" Residue "E ARG 650": "NH1" <-> "NH2" Residue "F ARG 327": "NH1" <-> "NH2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 342": "NH1" <-> "NH2" Residue "F ARG 362": "NH1" <-> "NH2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F ARG 417": "NH1" <-> "NH2" Residue "F ARG 475": "NH1" <-> "NH2" Residue "F ARG 510": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F ARG 554": "NH1" <-> "NH2" Residue "F ARG 555": "NH1" <-> "NH2" Residue "F ARG 561": "NH1" <-> "NH2" Residue "F ARG 590": "NH1" <-> "NH2" Residue "F ARG 594": "NH1" <-> "NH2" Residue "F ARG 603": "NH1" <-> "NH2" Residue "F ARG 620": "NH1" <-> "NH2" Residue "F ARG 628": "NH1" <-> "NH2" Residue "F ARG 629": "NH1" <-> "NH2" Residue "F ARG 650": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15697 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2464 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain breaks: 1 Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2517 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 1 Chain: "C" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2643 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2701 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "E" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2683 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2464 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 294} Chain breaks: 1 Chain: "P" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.25, per 1000 atoms: 0.53 Number of scatterers: 15697 At special positions: 0 Unit cell: (109.385, 146.125, 131.93, 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 54 16.00 P 14 15.00 Mg 4 11.99 O 2894 8.00 N 2841 7.00 C 9890 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: 6.33 Conformation dependent library (CDL) restraints added in 2.6 seconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 15 sheets defined 50.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 351 through 365 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 417 through 424 removed outlier: 3.946A pdb=" N ILE A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.208A pdb=" N GLN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.683A pdb=" N HIS A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.664A pdb=" N GLY A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 639 removed outlier: 3.569A pdb=" N ARG A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 634 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.898A pdb=" N HIS B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 417 through 424 removed outlier: 3.694A pdb=" N ILE B 424 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.586A pdb=" N THR B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN B 469 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 removed outlier: 3.709A pdb=" N GLN B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 552 removed outlier: 3.886A pdb=" N ARG B 546 " --> pdb=" O ASN B 543 " (cutoff:3.500A) Proline residue: B 547 - end of helix Processing helix chain 'B' and resid 556 through 561 Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 603 through 612 removed outlier: 3.784A pdb=" N GLY B 612 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 629 Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 339 through 345 removed outlier: 3.528A pdb=" N GLU C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 365 Processing helix chain 'C' and resid 387 through 398 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 461 through 473 removed outlier: 3.844A pdb=" N THR C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE C 466 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET C 467 " --> pdb=" O VAL C 463 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLN C 469 " --> pdb=" O THR C 465 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.983A pdb=" N LEU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN C 508 " --> pdb=" O GLN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 552 Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.987A pdb=" N ARG C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 595 Processing helix chain 'C' and resid 603 through 612 removed outlier: 3.736A pdb=" N ASP C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY C 612 " --> pdb=" O VAL C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 640 removed outlier: 4.787A pdb=" N VAL C 631 " --> pdb=" O ARG C 628 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN C 632 " --> pdb=" O ARG C 629 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 639 " --> pdb=" O ALA C 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 335 Processing helix chain 'D' and resid 339 through 346 removed outlier: 3.642A pdb=" N HIS D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 365 Processing helix chain 'D' and resid 387 through 399 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 411 through 413 No H-bonds generated for 'chain 'D' and resid 411 through 413' Processing helix chain 'D' and resid 417 through 424 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 461 through 473 removed outlier: 4.003A pdb=" N ILE D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET D 467 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 515 removed outlier: 3.726A pdb=" N GLU D 515 " --> pdb=" O GLN D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 543 No H-bonds generated for 'chain 'D' and resid 540 through 543' Processing helix chain 'D' and resid 545 through 553 Processing helix chain 'D' and resid 556 through 561 removed outlier: 3.554A pdb=" N ARG D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 603 through 612 removed outlier: 3.923A pdb=" N GLY D 612 " --> pdb=" O VAL D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 629 removed outlier: 3.625A pdb=" N ARG D 629 " --> pdb=" O VAL D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 637 Processing helix chain 'E' and resid 328 through 334 removed outlier: 3.575A pdb=" N ARG E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 346 removed outlier: 3.543A pdb=" N GLU E 345 " --> pdb=" O GLN E 341 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS E 346 " --> pdb=" O ARG E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 Processing helix chain 'E' and resid 387 through 399 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 411 through 413 No H-bonds generated for 'chain 'E' and resid 411 through 413' Processing helix chain 'E' and resid 417 through 424 removed outlier: 3.538A pdb=" N VAL E 420 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 456 through 458 No H-bonds generated for 'chain 'E' and resid 456 through 458' Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'E' and resid 499 through 516 Processing helix chain 'E' and resid 539 through 553 Proline residue: E 547 - end of helix Processing helix chain 'E' and resid 556 through 561 Processing helix chain 'E' and resid 573 through 595 Processing helix chain 'E' and resid 603 through 612 removed outlier: 3.873A pdb=" N GLY E 612 " --> pdb=" O VAL E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 629 removed outlier: 3.625A pdb=" N ARG E 629 " --> pdb=" O VAL E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 638 Processing helix chain 'F' and resid 328 through 336 Processing helix chain 'F' and resid 339 through 346 removed outlier: 4.034A pdb=" N HIS F 346 " --> pdb=" O ARG F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 365 Processing helix chain 'F' and resid 387 through 398 Processing helix chain 'F' and resid 411 through 413 No H-bonds generated for 'chain 'F' and resid 411 through 413' Processing helix chain 'F' and resid 419 through 422 No H-bonds generated for 'chain 'F' and resid 419 through 422' Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 456 through 458 No H-bonds generated for 'chain 'F' and resid 456 through 458' Processing helix chain 'F' and resid 461 through 470 removed outlier: 3.642A pdb=" N LEU F 468 " --> pdb=" O LEU F 464 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN F 469 " --> pdb=" O THR F 465 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 503 Processing helix chain 'F' and resid 507 through 510 No H-bonds generated for 'chain 'F' and resid 507 through 510' Processing helix chain 'F' and resid 549 through 553 Processing helix chain 'F' and resid 573 through 590 Processing helix chain 'F' and resid 594 through 596 No H-bonds generated for 'chain 'F' and resid 594 through 596' Processing helix chain 'F' and resid 602 through 611 removed outlier: 3.635A pdb=" N ASP F 611 " --> pdb=" O ASP F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 629 Processing helix chain 'F' and resid 631 through 639 Processing sheet with id= A, first strand: chain 'A' and resid 564 through 568 removed outlier: 4.051A pdb=" N GLY A 381 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= C, first strand: chain 'B' and resid 564 through 568 Processing sheet with id= D, first strand: chain 'B' and resid 475 through 477 Processing sheet with id= E, first strand: chain 'B' and resid 598 through 601 Processing sheet with id= F, first strand: chain 'C' and resid 564 through 568 removed outlier: 3.667A pdb=" N GLY C 381 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 475 through 477 Processing sheet with id= H, first strand: chain 'C' and resid 598 through 601 Processing sheet with id= I, first strand: chain 'D' and resid 564 through 568 Processing sheet with id= J, first strand: chain 'D' and resid 598 through 600 Processing sheet with id= K, first strand: chain 'E' and resid 564 through 568 Processing sheet with id= L, first strand: chain 'E' and resid 475 through 477 Processing sheet with id= M, first strand: chain 'E' and resid 597 through 600 removed outlier: 5.722A pdb=" N GLY E 645 " --> pdb=" O THR E 598 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU E 600 " --> pdb=" O GLY E 645 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS E 647 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR E 648 " --> pdb=" O GLN E 659 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 564 through 567 Processing sheet with id= O, first strand: chain 'F' and resid 474 through 477 removed outlier: 4.524A pdb=" N ILE F 484 " --> pdb=" O ARG F 475 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1755 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: 4.47 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5175 1.34 - 1.48: 3755 1.48 - 1.63: 6967 1.63 - 1.78: 18 1.78 - 1.93: 79 Bond restraints: 15994 Sorted by residual: bond pdb=" O2B AGS B 802 " pdb=" PB AGS B 802 " ideal model delta sigma weight residual 1.531 1.239 0.292 1.60e-02 3.91e+03 3.33e+02 bond pdb=" O2A AGS B 802 " pdb=" PA AGS B 802 " ideal model delta sigma weight residual 1.531 1.264 0.267 1.60e-02 3.91e+03 2.79e+02 bond pdb=" C8 AGS B 802 " pdb=" N9 AGS B 802 " ideal model delta sigma weight residual 1.370 1.190 0.180 1.10e-02 8.26e+03 2.69e+02 bond pdb=" C4 AGS B 802 " pdb=" N9 AGS B 802 " ideal model delta sigma weight residual 1.374 1.224 0.150 1.00e-02 1.00e+04 2.25e+02 bond pdb=" C3' AGS B 802 " pdb=" C4' AGS B 802 " ideal model delta sigma weight residual 1.526 1.390 0.136 1.10e-02 8.26e+03 1.54e+02 ... (remaining 15989 not shown) Histogram of bond angle deviations from ideal: 91.26 - 102.60: 51 102.60 - 113.95: 9469 113.95 - 125.29: 11743 125.29 - 136.64: 283 136.64 - 147.99: 2 Bond angle restraints: 21548 Sorted by residual: angle pdb=" C4 AGS E 801 " pdb=" N9 AGS E 801 " pdb=" C8 AGS E 801 " ideal model delta sigma weight residual 105.70 115.48 -9.78 4.55e-01 4.83e+00 4.62e+02 angle pdb=" C4 AGS C 802 " pdb=" N9 AGS C 802 " pdb=" C8 AGS C 802 " ideal model delta sigma weight residual 105.70 115.39 -9.69 4.55e-01 4.83e+00 4.53e+02 angle pdb=" C4 AGS B 802 " pdb=" N9 AGS B 802 " pdb=" C8 AGS B 802 " ideal model delta sigma weight residual 105.70 113.17 -7.47 4.55e-01 4.83e+00 2.70e+02 angle pdb=" N1 AGS B 802 " pdb=" C2 AGS B 802 " pdb=" N3 AGS B 802 " ideal model delta sigma weight residual 128.80 118.57 10.23 8.41e-01 1.41e+00 1.48e+02 angle pdb=" N7 AGS E 801 " pdb=" C8 AGS E 801 " pdb=" N9 AGS E 801 " ideal model delta sigma weight residual 114.03 105.71 8.32 6.99e-01 2.05e+00 1.42e+02 ... (remaining 21543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 9367 25.51 - 51.02: 318 51.02 - 76.54: 58 76.54 - 102.05: 7 102.05 - 127.56: 4 Dihedral angle restraints: 9754 sinusoidal: 4187 harmonic: 5567 Sorted by residual: dihedral pdb=" C4' ADP A 801 " pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -180.00 -52.79 -127.21 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" C2' ADP A 801 " pdb=" C1' ADP A 801 " pdb=" N9 ADP A 801 " pdb=" C4 ADP A 801 " ideal model delta sinusoidal sigma weight residual 91.55 -143.32 -125.13 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" C VAL B 653 " pdb=" N VAL B 653 " pdb=" CA VAL B 653 " pdb=" CB VAL B 653 " ideal model delta harmonic sigma weight residual -122.00 -134.99 12.99 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 9751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 2334 0.384 - 0.768: 3 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.920: 2 Chirality restraints: 2339 Sorted by residual: chirality pdb=" PB AGS B 802 " pdb=" O2B AGS B 802 " pdb=" O3A AGS B 802 " pdb=" O3B AGS B 802 " both_signs ideal model delta sigma weight residual True 3.18 -1.26 1.92 2.00e-01 2.50e+01 9.21e+01 chirality pdb=" PA AGS B 802 " pdb=" O2A AGS B 802 " pdb=" O3A AGS B 802 " pdb=" O5' AGS B 802 " both_signs ideal model delta sigma weight residual True 3.18 -1.56 1.62 2.00e-01 2.50e+01 6.55e+01 chirality pdb=" C2' AGS B 802 " pdb=" C1' AGS B 802 " pdb=" C3' AGS B 802 " pdb=" O2' AGS B 802 " both_signs ideal model delta sigma weight residual False -2.67 -2.02 -0.66 2.00e-01 2.50e+01 1.07e+01 ... (remaining 2336 not shown) Planarity restraints: 2787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 423 " -0.102 2.00e-02 2.50e+03 6.39e-02 7.14e+01 pdb=" CG PHE B 423 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE B 423 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 PHE B 423 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE B 423 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 423 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 423 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AGS D 801 " -0.088 2.00e-02 2.50e+03 4.45e-02 5.44e+01 pdb=" C2 AGS D 801 " 0.041 2.00e-02 2.50e+03 pdb=" C4 AGS D 801 " -0.018 2.00e-02 2.50e+03 pdb=" C5 AGS D 801 " -0.016 2.00e-02 2.50e+03 pdb=" C6 AGS D 801 " -0.006 2.00e-02 2.50e+03 pdb=" C8 AGS D 801 " 0.068 2.00e-02 2.50e+03 pdb=" N1 AGS D 801 " 0.020 2.00e-02 2.50e+03 pdb=" N3 AGS D 801 " -0.002 2.00e-02 2.50e+03 pdb=" N6 AGS D 801 " -0.062 2.00e-02 2.50e+03 pdb=" N7 AGS D 801 " 0.011 2.00e-02 2.50e+03 pdb=" N9 AGS D 801 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 601 " -0.084 2.00e-02 2.50e+03 4.55e-02 5.16e+01 pdb=" CG TRP B 601 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 601 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 601 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 601 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP B 601 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 601 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 601 " -0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 601 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 601 " -0.059 2.00e-02 2.50e+03 ... (remaining 2784 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 80 2.41 - 3.03: 10364 3.03 - 3.66: 24035 3.66 - 4.28: 37253 4.28 - 4.90: 60849 Nonbonded interactions: 132581 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O2G AGS B 802 " model vdw 1.788 2.170 nonbonded pdb=" O1B AGS D 801 " pdb="MG MG D 802 " model vdw 1.905 2.170 nonbonded pdb=" O1A AGS D 801 " pdb="MG MG D 802 " model vdw 2.012 2.170 nonbonded pdb=" OE2 GLU D 455 " pdb="MG MG D 802 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR E 388 " pdb="MG MG E 802 " model vdw 2.161 2.170 ... (remaining 132576 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' and resid 327 through 653) selection = (chain 'B' and (resid 327 through 515 or resid 539 through 653)) selection = (chain 'C' and (resid 327 through 515 or resid 539 through 653)) selection = (chain 'D' and (resid 327 through 515 or resid 539 through 653)) selection = (chain 'E' and (resid 327 through 515 or resid 539 through 653)) selection = chain 'F' } 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: 4.230 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: 9.970 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 43.210 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 0.009 0.292 15994 Z= 0.609 Angle : 1.076 20.677 21548 Z= 0.733 Chirality : 0.079 1.920 2339 Planarity : 0.006 0.080 2787 Dihedral : 13.731 127.559 6142 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 0.30 % Allowed : 1.28 % Favored : 98.42 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.56 % 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: 1.27 (0.21), residues: 1888 helix: 1.46 (0.18), residues: 897 sheet: 0.59 (0.32), residues: 263 loop : 0.31 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.004 TRP B 601 HIS 0.012 0.001 HIS B 418 PHE 0.102 0.005 PHE B 423 TYR 0.075 0.002 TYR A 430 ARG 0.009 0.000 ARG D 620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 350 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 LYS cc_start: 0.6650 (tttp) cc_final: 0.6417 (mmtp) REVERT: A 505 HIS cc_start: 0.7331 (m170) cc_final: 0.6930 (m170) REVERT: A 581 ASN cc_start: 0.8261 (m-40) cc_final: 0.7724 (t0) REVERT: A 585 ASN cc_start: 0.8415 (m-40) cc_final: 0.7686 (m-40) REVERT: B 435 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6666 (mt-10) REVERT: B 505 HIS cc_start: 0.6573 (m-70) cc_final: 0.6098 (m-70) REVERT: B 600 LEU cc_start: 0.7858 (mt) cc_final: 0.7646 (mt) REVERT: B 650 ARG cc_start: 0.7987 (mtp85) cc_final: 0.6470 (pmt170) REVERT: C 484 ILE cc_start: 0.7660 (mm) cc_final: 0.7146 (pt) REVERT: C 487 LYS cc_start: 0.7391 (mttt) cc_final: 0.7131 (mttp) REVERT: C 538 LYS cc_start: 0.6853 (mmtt) cc_final: 0.6631 (ptmt) REVERT: C 650 ARG cc_start: 0.6901 (ttp80) cc_final: 0.6643 (ttm170) REVERT: C 658 LYS cc_start: 0.6719 (mtmt) cc_final: 0.6179 (mtpt) REVERT: D 336 ARG cc_start: 0.5222 (mmp80) cc_final: 0.4973 (mmp80) REVERT: D 404 LYS cc_start: 0.7946 (ptmt) cc_final: 0.7430 (pttt) REVERT: D 650 ARG cc_start: 0.6313 (mmt180) cc_final: 0.6084 (ppt170) REVERT: E 337 PHE cc_start: 0.6880 (t80) cc_final: 0.6415 (m-80) REVERT: E 469 GLN cc_start: 0.7328 (tm-30) cc_final: 0.7007 (tt0) REVERT: E 500 ASP cc_start: 0.8506 (m-30) cc_final: 0.8200 (m-30) REVERT: E 554 ARG cc_start: 0.6323 (mtm-85) cc_final: 0.6095 (mtm110) REVERT: E 666 LEU cc_start: 0.7070 (mt) cc_final: 0.6584 (mp) REVERT: F 398 MET cc_start: 0.7398 (mmp) cc_final: 0.7113 (tpt) REVERT: F 410 ASP cc_start: 0.5364 (t0) cc_final: 0.4906 (t70) REVERT: F 458 LYS cc_start: 0.4022 (mttt) cc_final: 0.3774 (mtpt) REVERT: F 493 MET cc_start: 0.6901 (mpp) cc_final: 0.6692 (mpp) REVERT: F 555 ARG cc_start: 0.4315 (ttt180) cc_final: 0.3816 (tmt90) REVERT: F 599 LEU cc_start: 0.6692 (mt) cc_final: 0.6463 (pp) REVERT: F 649 LEU cc_start: 0.7354 (mt) cc_final: 0.7141 (tp) outliers start: 5 outliers final: 4 residues processed: 353 average time/residue: 1.5242 time to fit residues: 584.7876 Evaluate side-chains 171 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain E residue 611 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN C 511 GLN C 595 HIS E 505 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 HIS F 624 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15994 Z= 0.273 Angle : 0.613 8.591 21548 Z= 0.310 Chirality : 0.042 0.155 2339 Planarity : 0.005 0.083 2787 Dihedral : 10.109 119.972 2193 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 2.61 % Allowed : 10.88 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 1.33 (0.21), residues: 1888 helix: 1.55 (0.18), residues: 887 sheet: 0.26 (0.30), residues: 274 loop : 0.45 (0.26), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 601 HIS 0.007 0.001 HIS F 460 PHE 0.019 0.002 PHE F 558 TYR 0.014 0.001 TYR A 638 ARG 0.013 0.001 ARG F 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 GLN cc_start: 0.8247 (mt0) cc_final: 0.7958 (mt0) REVERT: A 482 LYS cc_start: 0.6628 (tttp) cc_final: 0.6412 (mmtp) REVERT: A 487 LYS cc_start: 0.7654 (mtpt) cc_final: 0.7091 (mmtm) REVERT: A 505 HIS cc_start: 0.7121 (m170) cc_final: 0.6734 (m170) REVERT: A 544 VAL cc_start: 0.7513 (m) cc_final: 0.7105 (p) REVERT: A 555 ARG cc_start: 0.7643 (ptp-170) cc_final: 0.7173 (pmm150) REVERT: A 581 ASN cc_start: 0.8173 (m-40) cc_final: 0.7758 (t0) REVERT: A 590 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6288 (tmm-80) REVERT: B 435 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6885 (mt-10) REVERT: B 484 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7088 (pp) REVERT: B 650 ARG cc_start: 0.8000 (mtp85) cc_final: 0.6428 (pmt170) REVERT: C 348 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7558 (mt) REVERT: C 404 LYS cc_start: 0.7964 (pttm) cc_final: 0.7745 (ptmm) REVERT: C 444 LYS cc_start: 0.7955 (tttp) cc_final: 0.7609 (tttt) REVERT: C 487 LYS cc_start: 0.7590 (mttt) cc_final: 0.7212 (mttp) REVERT: C 538 LYS cc_start: 0.6668 (mmtt) cc_final: 0.6380 (ptmt) REVERT: C 556 ASP cc_start: 0.7190 (m-30) cc_final: 0.6750 (m-30) REVERT: C 611 ASP cc_start: 0.8162 (m-30) cc_final: 0.7846 (p0) REVERT: C 650 ARG cc_start: 0.6800 (ttp80) cc_final: 0.6562 (ttm170) REVERT: C 659 GLN cc_start: 0.7176 (mt0) cc_final: 0.6938 (mt0) REVERT: D 336 ARG cc_start: 0.5256 (mmp80) cc_final: 0.4980 (mmp80) REVERT: D 404 LYS cc_start: 0.7912 (ptmt) cc_final: 0.7379 (pttt) REVERT: D 650 ARG cc_start: 0.5911 (mmt180) cc_final: 0.5484 (mmt90) REVERT: E 337 PHE cc_start: 0.7031 (t80) cc_final: 0.6581 (m-80) REVERT: E 400 LYS cc_start: 0.7082 (mptt) cc_final: 0.6813 (mmtt) REVERT: E 413 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: E 602 ASP cc_start: 0.6732 (t70) cc_final: 0.6433 (t70) REVERT: E 650 ARG cc_start: 0.6241 (mmt180) cc_final: 0.5840 (mmp80) REVERT: E 666 LEU cc_start: 0.7261 (mt) cc_final: 0.6863 (mp) REVERT: F 398 MET cc_start: 0.7415 (mmp) cc_final: 0.7021 (tpt) REVERT: F 410 ASP cc_start: 0.5090 (t0) cc_final: 0.4874 (t70) REVERT: F 458 LYS cc_start: 0.4345 (mttt) cc_final: 0.4118 (mtpt) REVERT: F 490 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6868 (mp) REVERT: F 555 ARG cc_start: 0.4273 (ttt180) cc_final: 0.3907 (tmt90) REVERT: F 599 LEU cc_start: 0.6809 (mt) cc_final: 0.6526 (pp) outliers start: 43 outliers final: 18 residues processed: 229 average time/residue: 1.2718 time to fit residues: 323.1900 Evaluate side-chains 183 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 561 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS A 596 ASN C 552 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 15994 Z= 0.388 Angle : 0.636 9.407 21548 Z= 0.319 Chirality : 0.044 0.154 2339 Planarity : 0.005 0.049 2787 Dihedral : 9.835 125.874 2190 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.76 % Rotamer: Outliers : 3.34 % Allowed : 12.71 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.71 (0.20), residues: 1888 helix: 1.09 (0.18), residues: 891 sheet: 0.00 (0.31), residues: 268 loop : 0.05 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 368 HIS 0.008 0.001 HIS E 418 PHE 0.025 0.002 PHE E 568 TYR 0.022 0.002 TYR A 397 ARG 0.006 0.001 ARG D 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 171 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 GLN cc_start: 0.8256 (mt0) cc_final: 0.7929 (mt0) REVERT: A 505 HIS cc_start: 0.7205 (m170) cc_final: 0.6781 (m170) REVERT: A 555 ARG cc_start: 0.7693 (ptp-170) cc_final: 0.7315 (mpt180) REVERT: A 590 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6245 (tmm-80) REVERT: A 634 LEU cc_start: 0.8531 (mp) cc_final: 0.8323 (mt) REVERT: B 336 ARG cc_start: 0.7478 (ttp80) cc_final: 0.7133 (tmm-80) REVERT: B 484 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7195 (mp) REVERT: B 589 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7457 (tmtt) REVERT: B 592 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7516 (tptp) REVERT: B 650 ARG cc_start: 0.7820 (mtp85) cc_final: 0.6484 (pmt170) REVERT: C 372 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7287 (mt-10) REVERT: C 444 LYS cc_start: 0.7949 (tttp) cc_final: 0.7594 (tttt) REVERT: C 487 LYS cc_start: 0.7552 (mttt) cc_final: 0.7030 (mttp) REVERT: C 538 LYS cc_start: 0.6693 (mmtt) cc_final: 0.6409 (ptmt) REVERT: C 650 ARG cc_start: 0.6751 (ttp80) cc_final: 0.6535 (ttm170) REVERT: D 336 ARG cc_start: 0.4931 (mmp80) cc_final: 0.4573 (mmp80) REVERT: D 351 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: D 404 LYS cc_start: 0.7703 (ptmt) cc_final: 0.7260 (pttm) REVERT: D 417 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6979 (ttm-80) REVERT: D 516 MET cc_start: 0.5608 (pmm) cc_final: 0.5358 (pmm) REVERT: D 658 LYS cc_start: 0.7383 (tptp) cc_final: 0.6889 (mttt) REVERT: E 337 PHE cc_start: 0.7198 (t80) cc_final: 0.6599 (m-80) REVERT: E 413 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: E 602 ASP cc_start: 0.6827 (t70) cc_final: 0.6511 (t70) REVERT: E 650 ARG cc_start: 0.6068 (mmt180) cc_final: 0.5686 (mmp80) REVERT: E 666 LEU cc_start: 0.7383 (mt) cc_final: 0.6884 (mp) REVERT: F 368 TRP cc_start: 0.7618 (m100) cc_final: 0.6552 (m100) REVERT: F 373 HIS cc_start: 0.6638 (OUTLIER) cc_final: 0.6308 (t-90) REVERT: F 398 MET cc_start: 0.7467 (mmp) cc_final: 0.6904 (tpt) REVERT: F 416 GLU cc_start: 0.4302 (pm20) cc_final: 0.3575 (tp30) REVERT: F 458 LYS cc_start: 0.4476 (mttt) cc_final: 0.4170 (mtpt) REVERT: F 490 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6602 (mp) REVERT: F 598 THR cc_start: 0.6399 (m) cc_final: 0.6080 (p) outliers start: 55 outliers final: 21 residues processed: 209 average time/residue: 1.2948 time to fit residues: 299.8867 Evaluate side-chains 171 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 417 ARG Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.0010 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 173 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 164 optimal weight: 0.3980 chunk 49 optimal weight: 0.0770 overall best weight: 0.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 HIS A 496 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 HIS E 504 GLN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15994 Z= 0.169 Angle : 0.530 12.131 21548 Z= 0.268 Chirality : 0.039 0.152 2339 Planarity : 0.004 0.047 2787 Dihedral : 9.355 121.451 2188 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 2.74 % Allowed : 13.62 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.86 (0.20), residues: 1888 helix: 1.20 (0.18), residues: 900 sheet: -0.08 (0.31), residues: 266 loop : 0.21 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 601 HIS 0.007 0.001 HIS B 505 PHE 0.018 0.001 PHE F 558 TYR 0.019 0.001 TYR A 397 ARG 0.004 0.000 ARG F 561 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6813 (mpt) REVERT: A 445 GLN cc_start: 0.8333 (mt0) cc_final: 0.8046 (mt0) REVERT: A 487 LYS cc_start: 0.7683 (mtpt) cc_final: 0.7107 (mmtm) REVERT: A 505 HIS cc_start: 0.7184 (m170) cc_final: 0.6800 (m170) REVERT: A 544 VAL cc_start: 0.7568 (m) cc_final: 0.7174 (p) REVERT: A 555 ARG cc_start: 0.7670 (ptp-170) cc_final: 0.7331 (pmm150) REVERT: A 590 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6161 (tmm-80) REVERT: A 599 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7993 (pp) REVERT: B 336 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7229 (tmm-80) REVERT: B 484 ILE cc_start: 0.7471 (mp) cc_final: 0.7073 (pp) REVERT: B 552 HIS cc_start: 0.7384 (t70) cc_final: 0.7018 (t70) REVERT: B 589 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7530 (ttpt) REVERT: B 592 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7486 (tptp) REVERT: C 372 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7240 (mt-10) REVERT: C 444 LYS cc_start: 0.8056 (tttp) cc_final: 0.7718 (tttt) REVERT: C 484 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7027 (pp) REVERT: C 487 LYS cc_start: 0.7525 (mttt) cc_final: 0.7111 (mttp) REVERT: C 538 LYS cc_start: 0.6679 (mmtt) cc_final: 0.6417 (ptmt) REVERT: C 650 ARG cc_start: 0.6732 (ttp80) cc_final: 0.6470 (ttm170) REVERT: D 336 ARG cc_start: 0.5067 (mmp80) cc_final: 0.4835 (mmp80) REVERT: D 404 LYS cc_start: 0.7784 (ptmt) cc_final: 0.7328 (pttm) REVERT: D 417 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6999 (ttm-80) REVERT: D 435 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7552 (mt-10) REVERT: E 413 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: E 500 ASP cc_start: 0.8417 (m-30) cc_final: 0.8097 (m-30) REVERT: E 602 ASP cc_start: 0.6748 (t70) cc_final: 0.6399 (t70) REVERT: E 643 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5391 (pt) REVERT: E 650 ARG cc_start: 0.6275 (mmt180) cc_final: 0.5953 (mmp80) REVERT: E 666 LEU cc_start: 0.7395 (mt) cc_final: 0.6891 (mp) REVERT: F 368 TRP cc_start: 0.7661 (m100) cc_final: 0.6523 (m100) REVERT: F 373 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.6233 (t-90) REVERT: F 398 MET cc_start: 0.7518 (mmp) cc_final: 0.6906 (tpt) REVERT: F 416 GLU cc_start: 0.4120 (pm20) cc_final: 0.3625 (tp30) REVERT: F 458 LYS cc_start: 0.4590 (mttt) cc_final: 0.4297 (mtpt) REVERT: F 475 ARG cc_start: 0.6767 (mmm-85) cc_final: 0.6341 (tpp-160) REVERT: F 490 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6757 (mp) outliers start: 45 outliers final: 18 residues processed: 196 average time/residue: 1.3068 time to fit residues: 283.4026 Evaluate side-chains 170 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 417 ARG Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 HIS A 596 ASN B 504 GLN B 633 GLN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15994 Z= 0.272 Angle : 0.573 17.668 21548 Z= 0.284 Chirality : 0.041 0.208 2339 Planarity : 0.004 0.048 2787 Dihedral : 9.574 122.048 2188 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 3.04 % Allowed : 14.47 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.69 (0.20), residues: 1888 helix: 1.07 (0.18), residues: 901 sheet: -0.19 (0.31), residues: 269 loop : 0.12 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 601 HIS 0.010 0.001 HIS B 505 PHE 0.020 0.001 PHE D 540 TYR 0.020 0.001 TYR A 397 ARG 0.007 0.000 ARG D 650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 147 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6818 (mpt) REVERT: A 445 GLN cc_start: 0.8303 (mt0) cc_final: 0.7986 (mt0) REVERT: A 505 HIS cc_start: 0.7226 (m170) cc_final: 0.6830 (m170) REVERT: A 599 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7952 (pp) REVERT: A 634 LEU cc_start: 0.8388 (mt) cc_final: 0.8080 (mp) REVERT: B 336 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7210 (tmm-80) REVERT: B 484 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7030 (pp) REVERT: B 552 HIS cc_start: 0.7455 (t70) cc_final: 0.7125 (t70) REVERT: B 592 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7485 (tptp) REVERT: C 372 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7228 (mt-10) REVERT: C 444 LYS cc_start: 0.7960 (tttp) cc_final: 0.7600 (tttt) REVERT: C 484 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7050 (pp) REVERT: C 487 LYS cc_start: 0.7492 (mttt) cc_final: 0.7091 (mttp) REVERT: C 538 LYS cc_start: 0.6780 (mmtt) cc_final: 0.6514 (ptmt) REVERT: C 602 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6805 (m-30) REVERT: C 650 ARG cc_start: 0.6734 (ttp80) cc_final: 0.6469 (ttm-80) REVERT: D 336 ARG cc_start: 0.5075 (mmp80) cc_final: 0.4861 (mmp80) REVERT: D 351 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: D 404 LYS cc_start: 0.7807 (ptmt) cc_final: 0.7342 (pttm) REVERT: D 435 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7568 (mt-10) REVERT: D 640 GLN cc_start: 0.6932 (mm-40) cc_final: 0.6560 (mp-120) REVERT: E 413 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: E 500 ASP cc_start: 0.8363 (m-30) cc_final: 0.8079 (m-30) REVERT: E 602 ASP cc_start: 0.6836 (t70) cc_final: 0.6461 (t70) REVERT: E 643 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5577 (pt) REVERT: E 650 ARG cc_start: 0.6047 (mmt180) cc_final: 0.5713 (mmp80) REVERT: E 666 LEU cc_start: 0.7403 (mt) cc_final: 0.6867 (mp) REVERT: F 368 TRP cc_start: 0.7679 (m100) cc_final: 0.6536 (m100) REVERT: F 373 HIS cc_start: 0.6539 (OUTLIER) cc_final: 0.6189 (t-90) REVERT: F 398 MET cc_start: 0.7578 (mmp) cc_final: 0.6952 (tpt) REVERT: F 416 GLU cc_start: 0.4268 (pm20) cc_final: 0.3722 (tp30) REVERT: F 458 LYS cc_start: 0.4670 (mttt) cc_final: 0.4318 (mtpt) REVERT: F 475 ARG cc_start: 0.6676 (mmm-85) cc_final: 0.6169 (ttm170) REVERT: F 490 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6641 (mp) outliers start: 50 outliers final: 21 residues processed: 184 average time/residue: 1.3810 time to fit residues: 281.8769 Evaluate side-chains 170 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain F residue 605 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 HIS B 593 GLN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15994 Z= 0.206 Angle : 0.546 14.345 21548 Z= 0.276 Chirality : 0.039 0.156 2339 Planarity : 0.004 0.047 2787 Dihedral : 9.080 119.124 2186 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 2.55 % Allowed : 15.14 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.75 (0.20), residues: 1888 helix: 1.07 (0.18), residues: 907 sheet: -0.17 (0.30), residues: 278 loop : 0.22 (0.26), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 601 HIS 0.010 0.001 HIS B 505 PHE 0.017 0.001 PHE D 540 TYR 0.020 0.001 TYR A 397 ARG 0.008 0.000 ARG D 650 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6817 (mpt) REVERT: A 445 GLN cc_start: 0.8374 (mt0) cc_final: 0.8033 (mt0) REVERT: A 505 HIS cc_start: 0.7239 (m170) cc_final: 0.6835 (m170) REVERT: A 599 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8012 (pp) REVERT: A 634 LEU cc_start: 0.8415 (mt) cc_final: 0.8103 (mp) REVERT: B 484 ILE cc_start: 0.7447 (mp) cc_final: 0.7060 (pp) REVERT: B 552 HIS cc_start: 0.7477 (t70) cc_final: 0.7195 (t70) REVERT: B 589 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7739 (tmtm) REVERT: B 592 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7488 (tptp) REVERT: C 372 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7260 (mt-10) REVERT: C 444 LYS cc_start: 0.8029 (tttp) cc_final: 0.7670 (tttt) REVERT: C 484 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7067 (pp) REVERT: C 487 LYS cc_start: 0.7526 (mttt) cc_final: 0.7016 (mttp) REVERT: C 538 LYS cc_start: 0.6765 (mmtt) cc_final: 0.6506 (ptmt) REVERT: C 625 GLU cc_start: 0.6468 (tp30) cc_final: 0.6199 (tp30) REVERT: C 650 ARG cc_start: 0.6725 (ttp80) cc_final: 0.6452 (ttm170) REVERT: D 404 LYS cc_start: 0.7833 (ptmt) cc_final: 0.7374 (pttm) REVERT: D 435 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7562 (mt-10) REVERT: E 413 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: E 500 ASP cc_start: 0.8366 (m-30) cc_final: 0.8088 (m-30) REVERT: E 602 ASP cc_start: 0.6791 (t70) cc_final: 0.6426 (t70) REVERT: E 643 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.5620 (pt) REVERT: E 650 ARG cc_start: 0.6169 (mmt180) cc_final: 0.5853 (mmp80) REVERT: E 666 LEU cc_start: 0.7388 (mt) cc_final: 0.6848 (mp) REVERT: F 368 TRP cc_start: 0.7764 (m100) cc_final: 0.6511 (m100) REVERT: F 398 MET cc_start: 0.7607 (mmp) cc_final: 0.7001 (tpt) REVERT: F 416 GLU cc_start: 0.4326 (pm20) cc_final: 0.3783 (tp30) REVERT: F 458 LYS cc_start: 0.4896 (mttt) cc_final: 0.4571 (mtpt) REVERT: F 475 ARG cc_start: 0.6898 (mmm-85) cc_final: 0.6416 (ptm160) REVERT: F 490 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6686 (mp) outliers start: 42 outliers final: 22 residues processed: 176 average time/residue: 1.3033 time to fit residues: 254.0630 Evaluate side-chains 161 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 337 PHE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 657 ASP Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15994 Z= 0.233 Angle : 0.555 13.467 21548 Z= 0.279 Chirality : 0.040 0.159 2339 Planarity : 0.004 0.047 2787 Dihedral : 9.039 117.912 2186 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % Rotamer: Outliers : 2.49 % Allowed : 15.62 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.73 (0.20), residues: 1888 helix: 1.06 (0.18), residues: 909 sheet: -0.16 (0.30), residues: 277 loop : 0.19 (0.26), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 601 HIS 0.006 0.001 HIS B 505 PHE 0.030 0.001 PHE F 558 TYR 0.021 0.001 TYR A 397 ARG 0.019 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 138 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6801 (mpt) REVERT: A 445 GLN cc_start: 0.8392 (mt0) cc_final: 0.8074 (mt0) REVERT: A 505 HIS cc_start: 0.7302 (m170) cc_final: 0.6919 (m170) REVERT: A 599 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7998 (pp) REVERT: B 484 ILE cc_start: 0.7458 (mp) cc_final: 0.7051 (pp) REVERT: B 552 HIS cc_start: 0.7445 (t70) cc_final: 0.7173 (t70) REVERT: B 589 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7755 (tmtm) REVERT: B 592 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7519 (tptp) REVERT: B 611 ASP cc_start: 0.7917 (t0) cc_final: 0.7412 (m-30) REVERT: C 372 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7235 (mt-10) REVERT: C 444 LYS cc_start: 0.8028 (tttp) cc_final: 0.7663 (tttt) REVERT: C 484 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7067 (pp) REVERT: C 487 LYS cc_start: 0.7534 (mttt) cc_final: 0.7100 (mttp) REVERT: C 538 LYS cc_start: 0.6813 (mmtt) cc_final: 0.6541 (ptmt) REVERT: C 602 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6885 (m-30) REVERT: D 404 LYS cc_start: 0.7826 (ptmt) cc_final: 0.7364 (pttm) REVERT: D 435 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7516 (mt-10) REVERT: D 640 GLN cc_start: 0.6938 (mm-40) cc_final: 0.6553 (mm-40) REVERT: E 413 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: E 500 ASP cc_start: 0.8380 (m-30) cc_final: 0.8108 (m-30) REVERT: E 602 ASP cc_start: 0.6801 (t70) cc_final: 0.6410 (t70) REVERT: E 639 GLU cc_start: 0.4229 (OUTLIER) cc_final: 0.3939 (pm20) REVERT: E 643 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5726 (pt) REVERT: E 650 ARG cc_start: 0.5980 (mmt180) cc_final: 0.5711 (mmp80) REVERT: E 666 LEU cc_start: 0.7453 (mt) cc_final: 0.6897 (mp) REVERT: F 368 TRP cc_start: 0.7739 (m100) cc_final: 0.6494 (m100) REVERT: F 398 MET cc_start: 0.7574 (mmp) cc_final: 0.6965 (tpt) REVERT: F 416 GLU cc_start: 0.4253 (pm20) cc_final: 0.3859 (tp30) REVERT: F 458 LYS cc_start: 0.4946 (mttt) cc_final: 0.4614 (mtpt) REVERT: F 490 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6680 (mp) outliers start: 41 outliers final: 21 residues processed: 168 average time/residue: 1.3005 time to fit residues: 242.1602 Evaluate side-chains 160 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 657 ASP Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 639 GLU Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15994 Z= 0.235 Angle : 0.560 12.748 21548 Z= 0.282 Chirality : 0.040 0.159 2339 Planarity : 0.004 0.046 2787 Dihedral : 8.991 116.742 2186 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 2.37 % Allowed : 16.11 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.78 (0.20), residues: 1888 helix: 1.09 (0.18), residues: 907 sheet: -0.20 (0.30), residues: 278 loop : 0.26 (0.26), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 601 HIS 0.005 0.001 HIS B 505 PHE 0.026 0.001 PHE F 423 TYR 0.022 0.001 TYR A 397 ARG 0.012 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6876 (mpt) REVERT: A 445 GLN cc_start: 0.8386 (mt0) cc_final: 0.8093 (mt0) REVERT: A 505 HIS cc_start: 0.7253 (m170) cc_final: 0.6941 (m170) REVERT: A 634 LEU cc_start: 0.8452 (mt) cc_final: 0.8140 (mp) REVERT: B 484 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7053 (pp) REVERT: B 552 HIS cc_start: 0.7443 (t70) cc_final: 0.7163 (t70) REVERT: B 589 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7763 (tmtm) REVERT: B 592 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7519 (tptp) REVERT: B 611 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: C 372 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7237 (mt-10) REVERT: C 444 LYS cc_start: 0.8033 (tttp) cc_final: 0.7664 (tttt) REVERT: C 484 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7083 (pp) REVERT: C 487 LYS cc_start: 0.7531 (mttt) cc_final: 0.7101 (mttp) REVERT: C 538 LYS cc_start: 0.6832 (mmtt) cc_final: 0.6558 (ptmt) REVERT: C 625 GLU cc_start: 0.6529 (tp30) cc_final: 0.6320 (tp30) REVERT: D 404 LYS cc_start: 0.7786 (ptmt) cc_final: 0.7314 (pttm) REVERT: D 435 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7548 (mt-10) REVERT: D 640 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6570 (mm-40) REVERT: E 413 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: E 500 ASP cc_start: 0.8381 (m-30) cc_final: 0.8111 (m-30) REVERT: E 602 ASP cc_start: 0.6806 (t70) cc_final: 0.6419 (t70) REVERT: E 639 GLU cc_start: 0.4217 (OUTLIER) cc_final: 0.3873 (pm20) REVERT: E 643 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.5796 (pt) REVERT: E 650 ARG cc_start: 0.6160 (mmt180) cc_final: 0.5855 (mmp80) REVERT: E 666 LEU cc_start: 0.7329 (mt) cc_final: 0.6792 (mp) REVERT: F 368 TRP cc_start: 0.7767 (m100) cc_final: 0.6512 (m100) REVERT: F 398 MET cc_start: 0.7593 (mmp) cc_final: 0.6989 (tpt) REVERT: F 416 GLU cc_start: 0.4329 (pm20) cc_final: 0.3829 (tp30) REVERT: F 458 LYS cc_start: 0.4933 (mttt) cc_final: 0.4610 (mtpt) REVERT: F 490 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6668 (mp) outliers start: 39 outliers final: 19 residues processed: 168 average time/residue: 1.4288 time to fit residues: 267.6957 Evaluate side-chains 159 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 611 ASP Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 639 GLU Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 180 optimal weight: 0.2980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15994 Z= 0.248 Angle : 0.571 12.276 21548 Z= 0.289 Chirality : 0.041 0.193 2339 Planarity : 0.004 0.046 2787 Dihedral : 9.007 115.891 2186 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Rotamer: Outliers : 1.95 % Allowed : 16.72 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.74 (0.20), residues: 1888 helix: 1.07 (0.18), residues: 906 sheet: -0.28 (0.30), residues: 288 loop : 0.26 (0.26), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 601 HIS 0.005 0.001 HIS C 418 PHE 0.023 0.001 PHE F 558 TYR 0.029 0.001 TYR A 397 ARG 0.011 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6836 (mpt) REVERT: A 445 GLN cc_start: 0.8384 (mt0) cc_final: 0.8079 (mt0) REVERT: A 505 HIS cc_start: 0.7233 (m170) cc_final: 0.6916 (m170) REVERT: A 634 LEU cc_start: 0.8448 (mt) cc_final: 0.8124 (mp) REVERT: B 336 ARG cc_start: 0.7639 (ttt-90) cc_final: 0.7321 (tmm-80) REVERT: B 484 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7059 (pp) REVERT: B 552 HIS cc_start: 0.7529 (t70) cc_final: 0.7242 (t70) REVERT: B 589 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7740 (tmtm) REVERT: B 592 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7521 (tptp) REVERT: B 611 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: C 330 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6360 (mp0) REVERT: C 372 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7238 (mt-10) REVERT: C 444 LYS cc_start: 0.8030 (tttp) cc_final: 0.7656 (tttt) REVERT: C 484 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7078 (pp) REVERT: C 487 LYS cc_start: 0.7518 (mttt) cc_final: 0.7091 (mttp) REVERT: C 538 LYS cc_start: 0.6828 (mmtt) cc_final: 0.6549 (ptmt) REVERT: C 625 GLU cc_start: 0.6517 (tp30) cc_final: 0.6304 (tp30) REVERT: D 404 LYS cc_start: 0.7758 (ptmt) cc_final: 0.7316 (pttm) REVERT: D 435 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7548 (mt-10) REVERT: D 640 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6563 (mm-40) REVERT: E 413 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: E 500 ASP cc_start: 0.8380 (m-30) cc_final: 0.8113 (m-30) REVERT: E 602 ASP cc_start: 0.6810 (t70) cc_final: 0.6440 (t70) REVERT: E 639 GLU cc_start: 0.4209 (OUTLIER) cc_final: 0.3842 (pm20) REVERT: E 643 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.5832 (pt) REVERT: E 650 ARG cc_start: 0.6117 (mmt180) cc_final: 0.5810 (mmp80) REVERT: E 666 LEU cc_start: 0.7354 (mt) cc_final: 0.6801 (mp) REVERT: F 368 TRP cc_start: 0.7774 (m100) cc_final: 0.6561 (m100) REVERT: F 398 MET cc_start: 0.7615 (mmp) cc_final: 0.6986 (tpt) REVERT: F 416 GLU cc_start: 0.4443 (pm20) cc_final: 0.3859 (tp30) REVERT: F 454 ASP cc_start: 0.6374 (p0) cc_final: 0.6081 (t70) REVERT: F 458 LYS cc_start: 0.4828 (mttt) cc_final: 0.4499 (mtpt) REVERT: F 490 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6628 (mp) outliers start: 32 outliers final: 21 residues processed: 165 average time/residue: 1.3466 time to fit residues: 246.1132 Evaluate side-chains 161 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 611 ASP Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 639 GLU Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 160 optimal weight: 0.0070 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15994 Z= 0.195 Angle : 0.552 12.183 21548 Z= 0.278 Chirality : 0.039 0.157 2339 Planarity : 0.004 0.045 2787 Dihedral : 8.859 112.948 2186 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 1.82 % Allowed : 16.96 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.84 (0.20), residues: 1888 helix: 1.20 (0.18), residues: 896 sheet: -0.23 (0.30), residues: 287 loop : 0.26 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 368 HIS 0.006 0.001 HIS F 460 PHE 0.022 0.001 PHE F 558 TYR 0.028 0.001 TYR A 397 ARG 0.009 0.000 ARG D 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6770 (mpt) REVERT: A 445 GLN cc_start: 0.8414 (mt0) cc_final: 0.8127 (mt0) REVERT: A 505 HIS cc_start: 0.7275 (m170) cc_final: 0.6975 (m170) REVERT: A 599 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8203 (pt) REVERT: A 634 LEU cc_start: 0.8450 (mt) cc_final: 0.8142 (mp) REVERT: B 336 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.7323 (tmm-80) REVERT: B 345 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7180 (mm-30) REVERT: B 484 ILE cc_start: 0.7500 (mp) cc_final: 0.7107 (pp) REVERT: B 552 HIS cc_start: 0.7596 (t70) cc_final: 0.6797 (m90) REVERT: B 589 LYS cc_start: 0.8140 (ttpt) cc_final: 0.7751 (tmtm) REVERT: B 592 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7517 (tptp) REVERT: B 611 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: C 330 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6397 (mp0) REVERT: C 372 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7245 (mt-10) REVERT: C 444 LYS cc_start: 0.7994 (tttp) cc_final: 0.7626 (tttt) REVERT: C 484 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7065 (pp) REVERT: C 487 LYS cc_start: 0.7517 (mttt) cc_final: 0.7096 (mttp) REVERT: C 538 LYS cc_start: 0.6844 (mmtt) cc_final: 0.6557 (ptmt) REVERT: C 625 GLU cc_start: 0.6476 (tp30) cc_final: 0.6248 (tp30) REVERT: D 404 LYS cc_start: 0.7821 (ptmt) cc_final: 0.7369 (pttm) REVERT: D 435 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7556 (mt-10) REVERT: D 640 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6639 (mm-40) REVERT: E 413 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: E 454 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: E 500 ASP cc_start: 0.8435 (m-30) cc_final: 0.8134 (m-30) REVERT: E 602 ASP cc_start: 0.6784 (t70) cc_final: 0.6428 (t70) REVERT: E 639 GLU cc_start: 0.4151 (OUTLIER) cc_final: 0.3791 (pm20) REVERT: E 643 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.5877 (pt) REVERT: E 650 ARG cc_start: 0.6260 (mmt180) cc_final: 0.5938 (mmp80) REVERT: E 666 LEU cc_start: 0.7381 (mt) cc_final: 0.6849 (mp) REVERT: F 368 TRP cc_start: 0.7896 (m100) cc_final: 0.6711 (m100) REVERT: F 398 MET cc_start: 0.7625 (mmp) cc_final: 0.7014 (tpt) REVERT: F 454 ASP cc_start: 0.6320 (p0) cc_final: 0.6066 (t70) REVERT: F 458 LYS cc_start: 0.4823 (mttt) cc_final: 0.4497 (mtpt) REVERT: F 490 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6629 (mp) REVERT: F 555 ARG cc_start: 0.4017 (ttt180) cc_final: 0.3359 (tmt90) outliers start: 30 outliers final: 20 residues processed: 168 average time/residue: 1.3564 time to fit residues: 252.0334 Evaluate side-chains 162 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 611 ASP Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 657 ASP Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 504 GLN Chi-restraints excluded: chain E residue 639 GLU Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 HIS ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.162557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102145 restraints weight = 21624.795| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.23 r_work: 0.3113 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15994 Z= 0.258 Angle : 0.575 11.932 21548 Z= 0.289 Chirality : 0.041 0.158 2339 Planarity : 0.004 0.046 2787 Dihedral : 8.960 114.091 2186 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Rotamer: Outliers : 1.95 % Allowed : 17.14 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.74 (0.20), residues: 1888 helix: 1.07 (0.18), residues: 908 sheet: -0.23 (0.30), residues: 286 loop : 0.24 (0.26), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 601 HIS 0.005 0.001 HIS C 418 PHE 0.020 0.001 PHE F 558 TYR 0.030 0.001 TYR A 397 ARG 0.013 0.000 ARG D 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5774.60 seconds wall clock time: 104 minutes 28.31 seconds (6268.31 seconds total)