Starting phenix.real_space_refine on Wed Mar 20 07:53:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3i_25659/03_2024/7t3i_25659_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3i_25659/03_2024/7t3i_25659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3i_25659/03_2024/7t3i_25659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3i_25659/03_2024/7t3i_25659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3i_25659/03_2024/7t3i_25659_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3i_25659/03_2024/7t3i_25659_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 123 5.16 5 C 16704 2.51 5 N 4786 2.21 5 O 5161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A ASP 718": "OD1" <-> "OD2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B ASP 612": "OD1" <-> "OD2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 749": "OE1" <-> "OE2" Residue "B GLU 778": "OE1" <-> "OE2" Residue "C ASP 203": "OD1" <-> "OD2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C ASP 410": "OD1" <-> "OD2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C GLU 628": "OE1" <-> "OE2" Residue "C TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 772": "OE1" <-> "OE2" Residue "D ASP 209": "OD1" <-> "OD2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 718": "OD1" <-> "OD2" Residue "D ASP 735": "OD1" <-> "OD2" Residue "D GLU 778": "OE1" <-> "OE2" Residue "D TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 209": "OD1" <-> "OD2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 286": "OD1" <-> "OD2" Residue "E GLU 312": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 374": "OE1" <-> "OE2" Residue "E TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E GLU 578": "OE1" <-> "OE2" Residue "E GLU 628": "OE1" <-> "OE2" Residue "E ASP 630": "OD1" <-> "OD2" Residue "E GLU 652": "OE1" <-> "OE2" Residue "E GLU 749": "OE1" <-> "OE2" Residue "E GLU 786": "OE1" <-> "OE2" Residue "F TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 441": "OD1" <-> "OD2" Residue "F ASP 497": "OD1" <-> "OD2" Residue "F TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 648": "OD1" <-> "OD2" Residue "F GLU 652": "OE1" <-> "OE2" Residue "F GLU 769": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26799 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4437 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 545} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4443 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4433 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4443 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 4412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4412 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 542} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4243 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 523} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 135 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'ATP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.51, per 1000 atoms: 0.50 Number of scatterers: 26799 At special positions: 0 Unit cell: (151.152, 145.904, 117.563, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 P 25 15.00 O 5161 8.00 N 4786 7.00 C 16704 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.81 Conformation dependent library (CDL) restraints added in 4.5 seconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6432 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 12 sheets defined 50.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 319 through 335 removed outlier: 3.933A pdb=" N MET A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 4.286A pdb=" N ARG A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 437 removed outlier: 4.139A pdb=" N ALA A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.723A pdb=" N HIS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 3.606A pdb=" N SER A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.759A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 619 through 631 Processing helix chain 'A' and resid 671 through 683 removed outlier: 3.865A pdb=" N VAL A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 723 removed outlier: 4.302A pdb=" N GLU A 720 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.719A pdb=" N GLU A 781 " --> pdb=" O MET A 777 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 208 through 223 removed outlier: 4.740A pdb=" N PHE B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 249 through 260 removed outlier: 3.628A pdb=" N HIS B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 304 through 307 No H-bonds generated for 'chain 'B' and resid 304 through 307' Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.866A pdb=" N ASP B 331 " --> pdb=" O MET B 327 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.776A pdb=" N ARG B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 396 through 402 removed outlier: 3.506A pdb=" N MET B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 437 removed outlier: 4.529A pdb=" N ALA B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.535A pdb=" N ALA B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 482 removed outlier: 3.568A pdb=" N SER B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 576 through 592 removed outlier: 4.454A pdb=" N GLU B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 581 " --> pdb=" O GLY B 577 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 606 No H-bonds generated for 'chain 'B' and resid 603 through 606' Processing helix chain 'B' and resid 617 through 630 removed outlier: 3.859A pdb=" N ASN B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 671 through 683 removed outlier: 4.099A pdb=" N VAL B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 723 Processing helix chain 'B' and resid 726 through 728 No H-bonds generated for 'chain 'B' and resid 726 through 728' Processing helix chain 'B' and resid 733 through 761 removed outlier: 3.510A pdb=" N GLY B 737 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 786 removed outlier: 3.871A pdb=" N ASN B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU B 786 " --> pdb=" O LYS B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 797 Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 208 through 223 removed outlier: 3.661A pdb=" N LYS C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 269 through 272 removed outlier: 3.522A pdb=" N VAL C 272 " --> pdb=" O ALA C 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 269 through 272' Processing helix chain 'C' and resid 279 through 293 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.621A pdb=" N ARG C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 331 " --> pdb=" O MET C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.560A pdb=" N ARG C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 387 removed outlier: 4.878A pdb=" N ASP C 387 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 437 removed outlier: 4.027A pdb=" N ALA C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 428 " --> pdb=" O GLN C 424 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 473 through 482 removed outlier: 3.871A pdb=" N SER C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 482 " --> pdb=" O LYS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 490 No H-bonds generated for 'chain 'C' and resid 488 through 490' Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 507 through 516 Processing helix chain 'C' and resid 518 through 522 Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 576 through 592 removed outlier: 4.374A pdb=" N GLU C 580 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 583 " --> pdb=" O SER C 579 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 592 " --> pdb=" O SER C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 630 Processing helix chain 'C' and resid 671 through 685 removed outlier: 4.091A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 685 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 723 Processing helix chain 'C' and resid 726 through 728 No H-bonds generated for 'chain 'C' and resid 726 through 728' Processing helix chain 'C' and resid 733 through 761 removed outlier: 3.828A pdb=" N GLY C 737 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 784 Processing helix chain 'C' and resid 794 through 798 removed outlier: 4.404A pdb=" N MET C 798 " --> pdb=" O GLU C 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 208 through 231 removed outlier: 4.042A pdb=" N LYS D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.184A pdb=" N GLY D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA D 227 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 260 removed outlier: 3.593A pdb=" N HIS D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 removed outlier: 3.884A pdb=" N VAL D 272 " --> pdb=" O ALA D 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 304 through 307 No H-bonds generated for 'chain 'D' and resid 304 through 307' Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.800A pdb=" N ASP D 331 " --> pdb=" O MET D 327 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 357 through 362 removed outlier: 3.809A pdb=" N ARG D 361 " --> pdb=" O PRO D 357 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 357 through 362' Processing helix chain 'D' and resid 374 through 386 removed outlier: 3.746A pdb=" N GLN D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 437 removed outlier: 4.130A pdb=" N ALA D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.635A pdb=" N HIS D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 482 removed outlier: 3.743A pdb=" N SER D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 502 No H-bonds generated for 'chain 'D' and resid 500 through 502' Processing helix chain 'D' and resid 507 through 516 Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 524 through 530 Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 576 through 592 removed outlier: 4.532A pdb=" N GLU D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 606 No H-bonds generated for 'chain 'D' and resid 603 through 606' Processing helix chain 'D' and resid 617 through 630 removed outlier: 4.159A pdb=" N VAL D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 671 through 683 removed outlier: 3.876A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 723 Processing helix chain 'D' and resid 726 through 728 No H-bonds generated for 'chain 'D' and resid 726 through 728' Processing helix chain 'D' and resid 733 through 761 removed outlier: 3.720A pdb=" N GLY D 737 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS D 758 " --> pdb=" O GLN D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 783 Processing helix chain 'D' and resid 794 through 796 No H-bonds generated for 'chain 'D' and resid 794 through 796' Processing helix chain 'E' and resid 201 through 203 No H-bonds generated for 'chain 'E' and resid 201 through 203' Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.884A pdb=" N ARG E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 223 removed outlier: 3.520A pdb=" N ARG E 223 " --> pdb=" O TRP E 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 219 through 223' Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 280 through 293 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 317 through 335 removed outlier: 3.511A pdb=" N VAL E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 408 through 437 removed outlier: 3.779A pdb=" N ALA E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.508A pdb=" N LEU E 455 " --> pdb=" O ARG E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 480 removed outlier: 3.581A pdb=" N VAL E 480 " --> pdb=" O PHE E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 502 No H-bonds generated for 'chain 'E' and resid 500 through 502' Processing helix chain 'E' and resid 507 through 516 Processing helix chain 'E' and resid 518 through 522 Processing helix chain 'E' and resid 524 through 530 removed outlier: 3.603A pdb=" N VAL E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 Processing helix chain 'E' and resid 569 through 571 No H-bonds generated for 'chain 'E' and resid 569 through 571' Processing helix chain 'E' and resid 578 through 592 removed outlier: 3.538A pdb=" N ALA E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 605 No H-bonds generated for 'chain 'E' and resid 603 through 605' Processing helix chain 'E' and resid 617 through 631 removed outlier: 3.590A pdb=" N VAL E 621 " --> pdb=" O ALA E 617 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR E 624 " --> pdb=" O ARG E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 649 No H-bonds generated for 'chain 'E' and resid 647 through 649' Processing helix chain 'E' and resid 672 through 683 removed outlier: 3.672A pdb=" N LEU E 678 " --> pdb=" O VAL E 675 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG E 683 " --> pdb=" O THR E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 724 removed outlier: 3.541A pdb=" N GLU E 720 " --> pdb=" O ASP E 716 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 755 Processing helix chain 'E' and resid 777 through 785 Processing helix chain 'F' and resid 200 through 203 No H-bonds generated for 'chain 'F' and resid 200 through 203' Processing helix chain 'F' and resid 208 through 222 removed outlier: 4.597A pdb=" N LYS F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Proline residue: F 221 - end of helix Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'F' and resid 249 through 260 Processing helix chain 'F' and resid 279 through 293 Processing helix chain 'F' and resid 304 through 307 Processing helix chain 'F' and resid 319 through 336 Processing helix chain 'F' and resid 352 through 354 No H-bonds generated for 'chain 'F' and resid 352 through 354' Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 408 through 437 removed outlier: 3.504A pdb=" N ALA F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN F 426 " --> pdb=" O SER F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.579A pdb=" N HIS F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 482 removed outlier: 3.698A pdb=" N SER F 481 " --> pdb=" O ARG F 477 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 482 " --> pdb=" O LYS F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 507 through 522 removed outlier: 4.836A pdb=" N GLY F 519 " --> pdb=" O MET F 515 " (cutoff:3.500A) Proline residue: F 520 - end of helix Processing helix chain 'F' and resid 524 through 530 removed outlier: 3.721A pdb=" N THR F 528 " --> pdb=" O PRO F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 Processing helix chain 'F' and resid 577 through 592 removed outlier: 3.899A pdb=" N ARG F 581 " --> pdb=" O GLY F 577 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 583 " --> pdb=" O SER F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 605 No H-bonds generated for 'chain 'F' and resid 603 through 605' Processing helix chain 'F' and resid 616 through 631 Processing helix chain 'F' and resid 647 through 649 No H-bonds generated for 'chain 'F' and resid 647 through 649' Processing helix chain 'F' and resid 652 through 655 No H-bonds generated for 'chain 'F' and resid 652 through 655' Processing helix chain 'F' and resid 671 through 684 removed outlier: 3.502A pdb=" N LYS F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 716 through 723 Processing helix chain 'F' and resid 733 through 760 removed outlier: 4.101A pdb=" N GLY F 737 " --> pdb=" O GLY F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 786 Processing sheet with id= A, first strand: chain 'A' and resid 365 through 368 removed outlier: 4.068A pdb=" N VAL A 365 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 345 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU A 241 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA A 347 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 344 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 263 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE A 300 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE A 265 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASP A 302 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 267 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 663 through 665 removed outlier: 8.525A pdb=" N ILE A 664 " --> pdb=" O GLY A 537 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 539 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 538 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL A 640 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU A 540 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLY A 642 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N CYS A 596 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE A 641 " --> pdb=" O CYS A 596 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU A 598 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA A 643 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE A 600 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASN A 562 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE A 599 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 564 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP A 601 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 566 " --> pdb=" O ASP A 601 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.394A pdb=" N VAL B 239 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 345 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 241 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 347 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA B 263 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE B 300 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 265 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP B 302 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL B 267 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 662 through 665 removed outlier: 4.334A pdb=" N THR B 662 " --> pdb=" O GLY B 537 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 539 " --> pdb=" O THR B 662 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ILE B 538 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 640 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 540 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY B 642 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS B 596 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE B 641 " --> pdb=" O CYS B 596 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU B 598 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA B 643 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE B 600 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN B 562 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N PHE B 599 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 564 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP B 601 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 566 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.567A pdb=" N ALA C 348 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA C 263 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N PHE C 300 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 265 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASP C 302 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL C 267 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 662 through 665 removed outlier: 4.079A pdb=" N THR C 662 " --> pdb=" O GLY C 537 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ILE C 538 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 640 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU C 540 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY C 642 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS C 596 " --> pdb=" O TYR C 639 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE C 641 " --> pdb=" O CYS C 596 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C 598 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA C 643 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE C 600 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN C 562 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE C 599 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE C 564 " --> pdb=" O PHE C 599 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP C 601 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 566 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.681A pdb=" N VAL D 365 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL D 239 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL D 345 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU D 241 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA D 347 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA D 263 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N PHE D 300 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE D 265 " --> pdb=" O PHE D 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 662 through 665 removed outlier: 3.948A pdb=" N THR D 662 " --> pdb=" O GLY D 537 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ILE D 538 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL D 640 " --> pdb=" O ILE D 538 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU D 540 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY D 642 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N CYS D 596 " --> pdb=" O TYR D 639 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE D 641 " --> pdb=" O CYS D 596 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 598 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA D 643 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE D 600 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASN D 562 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE D 599 " --> pdb=" O ASN D 562 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 564 " --> pdb=" O PHE D 599 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP D 601 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE D 566 " --> pdb=" O ASP D 601 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 365 through 369 removed outlier: 3.642A pdb=" N VAL E 365 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 345 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU E 241 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA E 347 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLY E 243 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR E 349 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL E 344 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA E 348 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA E 263 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE E 300 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 265 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP E 302 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL E 267 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 662 through 666 removed outlier: 3.654A pdb=" N THR E 662 " --> pdb=" O GLY E 537 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ILE E 538 " --> pdb=" O ILE E 638 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL E 640 " --> pdb=" O ILE E 538 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU E 540 " --> pdb=" O VAL E 640 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY E 642 " --> pdb=" O LEU E 540 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N GLY E 542 " --> pdb=" O GLY E 642 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N CYS E 596 " --> pdb=" O TYR E 639 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE E 641 " --> pdb=" O CYS E 596 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU E 598 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA E 643 " --> pdb=" O LEU E 598 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN E 562 " --> pdb=" O ILE E 597 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE E 599 " --> pdb=" O ASN E 562 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE E 564 " --> pdb=" O PHE E 599 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.758A pdb=" N VAL F 365 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS F 242 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N VAL F 239 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 345 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N LEU F 241 " --> pdb=" O VAL F 345 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA F 347 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N CYS F 297 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU F 346 " --> pdb=" O CYS F 297 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE F 299 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ALA F 348 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU F 301 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE F 265 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE F 300 " --> pdb=" O ILE F 265 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 663 through 666 removed outlier: 8.242A pdb=" N ILE F 664 " --> pdb=" O GLY F 537 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU F 539 " --> pdb=" O ILE F 664 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL F 666 " --> pdb=" O LEU F 539 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TRP F 541 " --> pdb=" O VAL F 666 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ILE F 538 " --> pdb=" O ILE F 638 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL F 640 " --> pdb=" O ILE F 538 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LEU F 540 " --> pdb=" O VAL F 640 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY F 642 " --> pdb=" O LEU F 540 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N GLY F 542 " --> pdb=" O GLY F 642 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS F 596 " --> pdb=" O TYR F 639 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE F 641 " --> pdb=" O CYS F 596 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU F 598 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA F 643 " --> pdb=" O LEU F 598 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE F 600 " --> pdb=" O ALA F 643 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 1016 hydrogen bonds defined for protein. 2997 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: 8.90 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9127 1.34 - 1.46: 5386 1.46 - 1.58: 12492 1.58 - 1.70: 32 1.70 - 1.82: 205 Bond restraints: 27242 Sorted by residual: bond pdb=" O3 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" O4 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" O2 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.46e+00 bond pdb=" O1 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.05e+00 ... (remaining 27237 not shown) Histogram of bond angle deviations from ideal: 98.75 - 106.99: 992 106.99 - 115.23: 16650 115.23 - 123.47: 18437 123.47 - 131.71: 758 131.71 - 139.95: 63 Bond angle restraints: 36900 Sorted by residual: angle pdb=" CA LEU C 660 " pdb=" CB LEU C 660 " pdb=" CG LEU C 660 " ideal model delta sigma weight residual 116.30 128.31 -12.01 3.50e+00 8.16e-02 1.18e+01 angle pdb=" CA PRO B 270 " pdb=" N PRO B 270 " pdb=" CD PRO B 270 " ideal model delta sigma weight residual 112.00 107.46 4.54 1.40e+00 5.10e-01 1.05e+01 angle pdb=" CG ARG B 321 " pdb=" CD ARG B 321 " pdb=" NE ARG B 321 " ideal model delta sigma weight residual 112.00 119.06 -7.06 2.20e+00 2.07e-01 1.03e+01 angle pdb=" C GLU F 217 " pdb=" N VAL F 218 " pdb=" CA VAL F 218 " ideal model delta sigma weight residual 123.16 119.86 3.30 1.06e+00 8.90e-01 9.70e+00 angle pdb=" N ILE F 654 " pdb=" CA ILE F 654 " pdb=" C ILE F 654 " ideal model delta sigma weight residual 111.90 109.41 2.49 8.10e-01 1.52e+00 9.41e+00 ... (remaining 36895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 15429 18.01 - 36.02: 1238 36.02 - 54.03: 171 54.03 - 72.04: 80 72.04 - 90.05: 24 Dihedral angle restraints: 16942 sinusoidal: 7009 harmonic: 9933 Sorted by residual: dihedral pdb=" CA GLU E 770 " pdb=" C GLU E 770 " pdb=" N ILE E 771 " pdb=" CA ILE E 771 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA THR F 494 " pdb=" C THR F 494 " pdb=" N ILE F 495 " pdb=" CA ILE F 495 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLU C 570 " pdb=" C GLU C 570 " pdb=" N LEU C 571 " pdb=" CA LEU C 571 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 16939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2880 0.036 - 0.072: 946 0.072 - 0.108: 296 0.108 - 0.144: 69 0.144 - 0.180: 5 Chirality restraints: 4196 Sorted by residual: chirality pdb=" CA GLN F 448 " pdb=" N GLN F 448 " pdb=" C GLN F 448 " pdb=" CB GLN F 448 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA GLN C 448 " pdb=" N GLN C 448 " pdb=" C GLN C 448 " pdb=" CB GLN C 448 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA VAL B 407 " pdb=" N VAL B 407 " pdb=" C VAL B 407 " pdb=" CB VAL B 407 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 4193 not shown) Planarity restraints: 4790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 484 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 485 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 484 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 485 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 485 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 485 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 356 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO F 357 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 357 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 357 " 0.029 5.00e-02 4.00e+02 ... (remaining 4787 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 474 2.66 - 3.22: 26490 3.22 - 3.78: 41538 3.78 - 4.34: 54186 4.34 - 4.90: 86300 Nonbonded interactions: 208988 Sorted by model distance: nonbonded pdb=" OG SER D 732 " pdb=" OD1 ASP D 735 " model vdw 2.101 2.440 nonbonded pdb=" OH TYR F 406 " pdb=" O VAL F 483 " model vdw 2.176 2.440 nonbonded pdb=" O TYR D 235 " pdb=" ND2 ASN D 342 " model vdw 2.187 2.520 nonbonded pdb=" OD1 ASN B 237 " pdb=" OG SER B 364 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR B 797 " pdb=" OE1 GLU C 652 " model vdw 2.219 2.440 ... (remaining 208983 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 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 460 or (resid 461 through 463 and (name N or nam \ e CA or name C or name O or name CB )) or resid 464 through 686 or resid 713 thr \ ough 761 or resid 770 through 790)) selection = (chain 'B' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'C' and (resid 199 through 272 or resid 277 through 309 or resid 318 thro \ ugh 460 or (resid 461 through 463 and (name N or name CA or name C or name O or \ name CB )) or resid 464 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'D' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'E' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'F' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 460 or (resid 461 \ through 463 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 4 through 761 or resid 770 through 790)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.020 Extract box with map and model: 5.080 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 66.600 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 27242 Z= 0.167 Angle : 0.587 12.015 36900 Z= 0.316 Chirality : 0.041 0.180 4196 Planarity : 0.004 0.067 4790 Dihedral : 13.812 90.047 10510 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.71 % Favored : 94.05 % Rotamer: Outliers : 0.07 % Allowed : 0.18 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.58 (0.15), residues: 3397 helix: 1.34 (0.13), residues: 1717 sheet: 0.05 (0.28), residues: 342 loop : -0.73 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 453 HIS 0.002 0.000 HIS A 502 PHE 0.017 0.001 PHE A 731 TYR 0.035 0.001 TYR D 752 ARG 0.012 0.000 ARG D 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 449 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.9157 (tp) cc_final: 0.8774 (tt) REVERT: B 546 CYS cc_start: 0.8744 (m) cc_final: 0.8208 (m) REVERT: B 585 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 247 CYS cc_start: 0.8329 (m) cc_final: 0.8126 (m) REVERT: C 318 MET cc_start: 0.9066 (tmm) cc_final: 0.8713 (tmm) REVERT: C 368 ASP cc_start: 0.8666 (t70) cc_final: 0.8240 (t0) REVERT: C 369 MET cc_start: 0.8571 (ptm) cc_final: 0.8348 (ppp) REVERT: C 473 MET cc_start: 0.7722 (tpt) cc_final: 0.7407 (tpp) REVERT: C 574 LYS cc_start: 0.8903 (ptmt) cc_final: 0.8686 (ptmt) REVERT: D 204 ILE cc_start: 0.9122 (tt) cc_final: 0.8916 (pt) REVERT: D 281 GLU cc_start: 0.8927 (mp0) cc_final: 0.8467 (mp0) REVERT: D 416 LYS cc_start: 0.9044 (tppt) cc_final: 0.8426 (tppt) REVERT: D 740 MET cc_start: 0.7721 (tmm) cc_final: 0.7381 (tmm) REVERT: E 304 ILE cc_start: 0.9306 (tp) cc_final: 0.9096 (tp) REVERT: E 473 MET cc_start: 0.8619 (tpt) cc_final: 0.8332 (mmm) REVERT: E 515 MET cc_start: 0.8705 (tpp) cc_final: 0.8175 (tpp) REVERT: E 630 ASP cc_start: 0.7795 (t0) cc_final: 0.7308 (t0) REVERT: F 219 TRP cc_start: 0.5802 (t-100) cc_final: 0.5574 (t-100) REVERT: F 303 GLU cc_start: 0.6467 (mp0) cc_final: 0.5972 (mp0) REVERT: F 371 MET cc_start: 0.6999 (tmm) cc_final: 0.6638 (tmm) REVERT: F 745 GLN cc_start: 0.8713 (mt0) cc_final: 0.8310 (mt0) outliers start: 2 outliers final: 0 residues processed: 450 average time/residue: 0.3524 time to fit residues: 256.9773 Evaluate side-chains 320 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 20.0000 chunk 259 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 103 optimal weight: 0.3980 chunk 162 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 310 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN A 475 GLN B 426 ASN B 459 HIS ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 ASN D 585 GLN ** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27242 Z= 0.256 Angle : 0.559 8.897 36900 Z= 0.286 Chirality : 0.041 0.172 4196 Planarity : 0.005 0.069 4790 Dihedral : 9.975 84.104 4024 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.45 % Favored : 93.32 % Rotamer: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.50 (0.15), residues: 3397 helix: 1.30 (0.12), residues: 1777 sheet: -0.16 (0.28), residues: 344 loop : -0.87 (0.19), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 219 HIS 0.004 0.001 HIS E 438 PHE 0.022 0.002 PHE D 354 TYR 0.016 0.001 TYR D 413 ARG 0.010 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 397 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8649 (m-30) cc_final: 0.8010 (p0) REVERT: A 473 MET cc_start: 0.8803 (tpp) cc_final: 0.8086 (tpp) REVERT: A 546 CYS cc_start: 0.8936 (m) cc_final: 0.8625 (m) REVERT: B 242 HIS cc_start: 0.9059 (p90) cc_final: 0.8835 (p90) REVERT: B 401 LYS cc_start: 0.9208 (mttt) cc_final: 0.8969 (tppt) REVERT: B 546 CYS cc_start: 0.8750 (m) cc_final: 0.8296 (m) REVERT: B 585 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8455 (tm-30) REVERT: B 660 LEU cc_start: 0.9420 (pt) cc_final: 0.9214 (pp) REVERT: B 740 MET cc_start: 0.8497 (tmm) cc_final: 0.8274 (tmm) REVERT: C 318 MET cc_start: 0.8741 (tmm) cc_final: 0.8380 (tmm) REVERT: C 368 ASP cc_start: 0.8618 (t70) cc_final: 0.8370 (t0) REVERT: C 369 MET cc_start: 0.8616 (ptm) cc_final: 0.8128 (ptt) REVERT: C 473 MET cc_start: 0.7698 (tpt) cc_final: 0.7440 (tpp) REVERT: C 493 SER cc_start: 0.9068 (m) cc_final: 0.8816 (p) REVERT: C 574 LYS cc_start: 0.8972 (ptmt) cc_final: 0.8724 (ptmt) REVERT: C 652 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7521 (mt-10) REVERT: C 741 GLN cc_start: 0.8269 (tp40) cc_final: 0.8000 (tp40) REVERT: D 231 MET cc_start: 0.6770 (tpp) cc_final: 0.6521 (tpt) REVERT: D 281 GLU cc_start: 0.9043 (mp0) cc_final: 0.8480 (mp0) REVERT: D 416 LYS cc_start: 0.9020 (tppt) cc_final: 0.8232 (tppt) REVERT: D 466 TRP cc_start: 0.6804 (p90) cc_final: 0.6489 (p90) REVERT: D 580 GLU cc_start: 0.8825 (mp0) cc_final: 0.8347 (mp0) REVERT: D 649 MET cc_start: 0.8022 (tpt) cc_final: 0.7672 (tpp) REVERT: D 740 MET cc_start: 0.7777 (tmm) cc_final: 0.7401 (tmm) REVERT: E 515 MET cc_start: 0.8682 (tpp) cc_final: 0.8174 (tpp) REVERT: E 553 LYS cc_start: 0.9408 (mttp) cc_final: 0.8697 (mttt) REVERT: E 626 LEU cc_start: 0.8854 (mm) cc_final: 0.8383 (mm) REVERT: F 219 TRP cc_start: 0.5757 (t-100) cc_final: 0.5555 (t-100) REVERT: F 303 GLU cc_start: 0.6432 (mp0) cc_final: 0.5858 (mp0) REVERT: F 371 MET cc_start: 0.7196 (tmm) cc_final: 0.6859 (tmm) REVERT: F 473 MET cc_start: 0.6934 (tmm) cc_final: 0.6628 (tmm) REVERT: F 603 MET cc_start: 0.8244 (tpp) cc_final: 0.7877 (tpp) REVERT: F 745 GLN cc_start: 0.8693 (mt0) cc_final: 0.8289 (mt0) outliers start: 1 outliers final: 0 residues processed: 398 average time/residue: 0.3424 time to fit residues: 222.5236 Evaluate side-chains 304 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 311 optimal weight: 6.9990 chunk 336 optimal weight: 9.9990 chunk 277 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 426 ASN B 459 HIS ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS ** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 HIS E 459 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27242 Z= 0.180 Angle : 0.526 9.724 36900 Z= 0.265 Chirality : 0.040 0.173 4196 Planarity : 0.004 0.053 4790 Dihedral : 9.768 81.856 4024 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.62 (0.15), residues: 3397 helix: 1.44 (0.13), residues: 1777 sheet: -0.24 (0.27), residues: 368 loop : -0.85 (0.19), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 453 HIS 0.005 0.001 HIS E 438 PHE 0.013 0.001 PHE C 731 TYR 0.037 0.001 TYR D 752 ARG 0.006 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 402 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8672 (m-30) cc_final: 0.8052 (p0) REVERT: A 546 CYS cc_start: 0.8900 (m) cc_final: 0.8577 (m) REVERT: A 576 VAL cc_start: 0.8305 (m) cc_final: 0.8096 (p) REVERT: B 401 LYS cc_start: 0.9208 (mttt) cc_final: 0.8950 (tppt) REVERT: B 546 CYS cc_start: 0.8725 (m) cc_final: 0.8151 (m) REVERT: B 585 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8567 (tm-30) REVERT: B 660 LEU cc_start: 0.9418 (pt) cc_final: 0.9174 (pp) REVERT: B 740 MET cc_start: 0.8492 (tmm) cc_final: 0.8240 (tmm) REVERT: C 318 MET cc_start: 0.8643 (tmm) cc_final: 0.8287 (tmm) REVERT: C 368 ASP cc_start: 0.8588 (t70) cc_final: 0.8369 (t0) REVERT: C 369 MET cc_start: 0.8525 (ptm) cc_final: 0.8097 (ptt) REVERT: C 452 ASP cc_start: 0.7192 (m-30) cc_final: 0.6949 (m-30) REVERT: C 525 GLU cc_start: 0.7784 (pm20) cc_final: 0.6985 (mt-10) REVERT: C 574 LYS cc_start: 0.8921 (ptmt) cc_final: 0.8662 (ptmt) REVERT: C 741 GLN cc_start: 0.8040 (tp40) cc_final: 0.7824 (tp40) REVERT: D 281 GLU cc_start: 0.9037 (mp0) cc_final: 0.8492 (mp0) REVERT: D 466 TRP cc_start: 0.6642 (p90) cc_final: 0.6200 (p90) REVERT: D 580 GLU cc_start: 0.8818 (mp0) cc_final: 0.8431 (mp0) REVERT: D 649 MET cc_start: 0.7942 (tpt) cc_final: 0.7660 (tpp) REVERT: D 740 MET cc_start: 0.7978 (tmm) cc_final: 0.7662 (tmm) REVERT: E 299 ILE cc_start: 0.9416 (mm) cc_final: 0.9044 (tp) REVERT: E 515 MET cc_start: 0.8747 (tpp) cc_final: 0.8226 (tpp) REVERT: E 626 LEU cc_start: 0.8895 (mm) cc_final: 0.8390 (mm) REVERT: E 630 ASP cc_start: 0.8100 (t70) cc_final: 0.7898 (t0) REVERT: F 303 GLU cc_start: 0.6458 (mp0) cc_final: 0.5886 (mp0) REVERT: F 371 MET cc_start: 0.7252 (tmm) cc_final: 0.6973 (tmm) REVERT: F 473 MET cc_start: 0.6751 (tmm) cc_final: 0.6428 (tmm) REVERT: F 603 MET cc_start: 0.8364 (tpp) cc_final: 0.7907 (tpp) REVERT: F 745 GLN cc_start: 0.8665 (mt0) cc_final: 0.8286 (mt0) outliers start: 3 outliers final: 1 residues processed: 405 average time/residue: 0.3697 time to fit residues: 245.7433 Evaluate side-chains 314 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 313 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 208 optimal weight: 0.0980 chunk 312 optimal weight: 5.9990 chunk 330 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 295 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN B 426 ASN C 412 GLN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN C 741 GLN C 745 GLN D 585 GLN ** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27242 Z= 0.329 Angle : 0.616 8.235 36900 Z= 0.312 Chirality : 0.042 0.195 4196 Planarity : 0.005 0.054 4790 Dihedral : 9.842 81.998 4024 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.33 % Favored : 92.46 % Rotamer: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.44 (0.15), residues: 3397 helix: 1.32 (0.12), residues: 1772 sheet: -0.23 (0.27), residues: 354 loop : -0.98 (0.19), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 219 HIS 0.005 0.001 HIS E 438 PHE 0.018 0.002 PHE D 288 TYR 0.035 0.002 TYR D 752 ARG 0.006 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 379 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 CYS cc_start: 0.8916 (m) cc_final: 0.8614 (m) REVERT: A 576 VAL cc_start: 0.8302 (m) cc_final: 0.8095 (p) REVERT: B 319 GLU cc_start: 0.8186 (pm20) cc_final: 0.7775 (pm20) REVERT: B 546 CYS cc_start: 0.8812 (m) cc_final: 0.8343 (m) REVERT: B 603 MET cc_start: 0.8199 (mmt) cc_final: 0.7942 (mmp) REVERT: B 628 GLU cc_start: 0.8645 (mm-30) cc_final: 0.7814 (mm-30) REVERT: B 740 MET cc_start: 0.8634 (tmm) cc_final: 0.8351 (tmm) REVERT: B 797 TYR cc_start: 0.7309 (m-10) cc_final: 0.7092 (m-10) REVERT: C 247 CYS cc_start: 0.8369 (m) cc_final: 0.8166 (m) REVERT: C 318 MET cc_start: 0.8695 (tmm) cc_final: 0.8288 (tmm) REVERT: C 369 MET cc_start: 0.8564 (ptm) cc_final: 0.8148 (ptt) REVERT: C 473 MET cc_start: 0.7572 (tpt) cc_final: 0.7312 (tpp) REVERT: C 574 LYS cc_start: 0.8997 (ptmt) cc_final: 0.8759 (ptmt) REVERT: C 741 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7814 (tp-100) REVERT: D 231 MET cc_start: 0.6866 (tpp) cc_final: 0.6652 (tpt) REVERT: D 350 ASN cc_start: 0.9307 (m-40) cc_final: 0.9035 (m-40) REVERT: D 580 GLU cc_start: 0.8713 (mp0) cc_final: 0.8341 (mp0) REVERT: D 740 MET cc_start: 0.7972 (tmm) cc_final: 0.7578 (tmm) REVERT: E 515 MET cc_start: 0.8752 (tpp) cc_final: 0.8226 (tpp) REVERT: E 626 LEU cc_start: 0.9050 (mm) cc_final: 0.8560 (mm) REVERT: E 630 ASP cc_start: 0.8149 (t70) cc_final: 0.7940 (t0) REVERT: F 219 TRP cc_start: 0.6016 (t-100) cc_final: 0.5688 (t-100) REVERT: F 303 GLU cc_start: 0.6455 (mp0) cc_final: 0.5833 (mp0) REVERT: F 371 MET cc_start: 0.7327 (tmm) cc_final: 0.7043 (tmm) REVERT: F 473 MET cc_start: 0.6839 (tmm) cc_final: 0.6463 (tmm) REVERT: F 482 LEU cc_start: 0.8959 (mt) cc_final: 0.8720 (tt) REVERT: F 603 MET cc_start: 0.8353 (tpp) cc_final: 0.7910 (tpp) outliers start: 4 outliers final: 1 residues processed: 383 average time/residue: 0.3482 time to fit residues: 218.6026 Evaluate side-chains 299 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 298 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 246 optimal weight: 0.0970 chunk 136 optimal weight: 0.7980 chunk 282 optimal weight: 1.9990 chunk 228 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 168 optimal weight: 0.0870 chunk 296 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN B 426 ASN B 459 HIS C 412 GLN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN ** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 HIS ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27242 Z= 0.139 Angle : 0.527 12.681 36900 Z= 0.262 Chirality : 0.041 0.202 4196 Planarity : 0.004 0.055 4790 Dihedral : 9.393 86.640 4024 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.59 % Favored : 94.20 % Rotamer: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.68 (0.15), residues: 3397 helix: 1.53 (0.13), residues: 1757 sheet: -0.22 (0.27), residues: 362 loop : -0.83 (0.19), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 780 HIS 0.007 0.000 HIS E 438 PHE 0.014 0.001 PHE A 731 TYR 0.037 0.001 TYR D 752 ARG 0.004 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 418 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8708 (m-30) cc_final: 0.8497 (m-30) REVERT: A 546 CYS cc_start: 0.8807 (m) cc_final: 0.8473 (m) REVERT: A 576 VAL cc_start: 0.8241 (m) cc_final: 0.8011 (p) REVERT: B 319 GLU cc_start: 0.8080 (pm20) cc_final: 0.7646 (pm20) REVERT: B 401 LYS cc_start: 0.9164 (mttt) cc_final: 0.8839 (tppt) REVERT: B 546 CYS cc_start: 0.8711 (m) cc_final: 0.8127 (m) REVERT: B 740 MET cc_start: 0.8538 (tmm) cc_final: 0.8271 (tmm) REVERT: C 369 MET cc_start: 0.8514 (ptm) cc_final: 0.8309 (ptt) REVERT: C 525 GLU cc_start: 0.7922 (pm20) cc_final: 0.7278 (mp0) REVERT: C 574 LYS cc_start: 0.8909 (ptmt) cc_final: 0.8636 (ptmt) REVERT: C 741 GLN cc_start: 0.7901 (tp-100) cc_final: 0.7683 (tp40) REVERT: D 286 ASP cc_start: 0.7481 (t0) cc_final: 0.7275 (t0) REVERT: D 413 TYR cc_start: 0.8275 (m-10) cc_final: 0.8073 (m-80) REVERT: D 466 TRP cc_start: 0.6580 (p90) cc_final: 0.5858 (p90) REVERT: D 580 GLU cc_start: 0.8715 (mp0) cc_final: 0.8387 (mp0) REVERT: D 740 MET cc_start: 0.8042 (tmm) cc_final: 0.7685 (tmm) REVERT: E 406 TYR cc_start: 0.7586 (m-10) cc_final: 0.7345 (m-10) REVERT: E 515 MET cc_start: 0.8765 (tpp) cc_final: 0.8223 (tpp) REVERT: E 626 LEU cc_start: 0.8962 (mm) cc_final: 0.8430 (mm) REVERT: E 777 MET cc_start: 0.7348 (mmp) cc_final: 0.6647 (mmt) REVERT: F 303 GLU cc_start: 0.6370 (mp0) cc_final: 0.5781 (mp0) REVERT: F 318 MET cc_start: 0.4825 (mmt) cc_final: 0.4518 (mmt) REVERT: F 371 MET cc_start: 0.7533 (tmm) cc_final: 0.7216 (tmm) REVERT: F 399 LEU cc_start: 0.9305 (mp) cc_final: 0.9098 (mp) REVERT: F 473 MET cc_start: 0.6886 (tmm) cc_final: 0.6523 (tmm) REVERT: F 482 LEU cc_start: 0.8930 (mt) cc_final: 0.8693 (tt) REVERT: F 585 GLN cc_start: 0.8681 (tt0) cc_final: 0.8448 (tp40) REVERT: F 603 MET cc_start: 0.8329 (tpp) cc_final: 0.7997 (tpp) REVERT: F 745 GLN cc_start: 0.8560 (mt0) cc_final: 0.8189 (mt0) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.3449 time to fit residues: 234.3454 Evaluate side-chains 315 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 0.7980 chunk 297 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 274 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 GLN B 426 ASN B 459 HIS ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27242 Z= 0.246 Angle : 0.555 9.786 36900 Z= 0.280 Chirality : 0.041 0.170 4196 Planarity : 0.004 0.057 4790 Dihedral : 9.436 86.374 4024 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.80 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.66 (0.15), residues: 3397 helix: 1.52 (0.13), residues: 1763 sheet: -0.24 (0.27), residues: 365 loop : -0.86 (0.19), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 219 HIS 0.003 0.001 HIS B 459 PHE 0.015 0.001 PHE B 220 TYR 0.035 0.001 TYR D 752 ARG 0.006 0.000 ARG B 635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 CYS cc_start: 0.8878 (m) cc_final: 0.8521 (m) REVERT: A 576 VAL cc_start: 0.8300 (m) cc_final: 0.8060 (p) REVERT: B 319 GLU cc_start: 0.8078 (pm20) cc_final: 0.7828 (pm20) REVERT: B 401 LYS cc_start: 0.9165 (mttt) cc_final: 0.8853 (tppt) REVERT: B 546 CYS cc_start: 0.8782 (m) cc_final: 0.8323 (m) REVERT: B 740 MET cc_start: 0.8576 (tmm) cc_final: 0.8244 (tmm) REVERT: C 369 MET cc_start: 0.8593 (ptm) cc_final: 0.8322 (ptt) REVERT: C 571 LEU cc_start: 0.8695 (mt) cc_final: 0.8442 (mt) REVERT: C 652 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 741 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7569 (tp-100) REVERT: D 286 ASP cc_start: 0.7622 (t0) cc_final: 0.7412 (t0) REVERT: D 466 TRP cc_start: 0.6734 (p90) cc_final: 0.5965 (p90) REVERT: D 580 GLU cc_start: 0.8715 (mp0) cc_final: 0.8364 (mp0) REVERT: D 740 MET cc_start: 0.8047 (tmm) cc_final: 0.7610 (tmm) REVERT: E 406 TYR cc_start: 0.7687 (m-10) cc_final: 0.7480 (m-10) REVERT: E 515 MET cc_start: 0.8773 (tpp) cc_final: 0.8203 (tpp) REVERT: E 596 CYS cc_start: 0.7693 (t) cc_final: 0.7478 (t) REVERT: E 626 LEU cc_start: 0.8775 (mm) cc_final: 0.8382 (mm) REVERT: E 777 MET cc_start: 0.7388 (mmp) cc_final: 0.6665 (mmt) REVERT: F 303 GLU cc_start: 0.6405 (mp0) cc_final: 0.5812 (mp0) REVERT: F 318 MET cc_start: 0.4708 (mmt) cc_final: 0.4488 (mmt) REVERT: F 371 MET cc_start: 0.7556 (tmm) cc_final: 0.7269 (tmm) REVERT: F 473 MET cc_start: 0.6834 (tmm) cc_final: 0.6458 (tmm) REVERT: F 585 GLN cc_start: 0.8711 (tt0) cc_final: 0.8472 (tp40) REVERT: F 603 MET cc_start: 0.8336 (tpp) cc_final: 0.7972 (tpp) REVERT: F 745 GLN cc_start: 0.8545 (mt0) cc_final: 0.8192 (mt0) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.3361 time to fit residues: 221.1060 Evaluate side-chains 313 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 278 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 329 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN B 426 ASN B 459 HIS ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN D 412 GLN E 438 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27242 Z= 0.188 Angle : 0.541 11.155 36900 Z= 0.272 Chirality : 0.041 0.171 4196 Planarity : 0.004 0.058 4790 Dihedral : 9.339 88.448 4024 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.51 % Favored : 93.29 % Rotamer: Outliers : 0.07 % Allowed : 1.66 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.68 (0.15), residues: 3397 helix: 1.53 (0.13), residues: 1761 sheet: -0.24 (0.27), residues: 367 loop : -0.84 (0.19), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 453 HIS 0.007 0.001 HIS E 438 PHE 0.022 0.001 PHE F 423 TYR 0.036 0.001 TYR D 752 ARG 0.005 0.000 ARG D 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8688 (m-30) cc_final: 0.7989 (p0) REVERT: A 546 CYS cc_start: 0.8836 (m) cc_final: 0.8480 (m) REVERT: A 576 VAL cc_start: 0.8257 (m) cc_final: 0.8028 (p) REVERT: B 319 GLU cc_start: 0.8060 (pm20) cc_final: 0.7803 (pm20) REVERT: B 401 LYS cc_start: 0.9164 (mttt) cc_final: 0.8839 (tppt) REVERT: B 546 CYS cc_start: 0.8754 (m) cc_final: 0.8244 (m) REVERT: B 603 MET cc_start: 0.7805 (mmp) cc_final: 0.7512 (mmp) REVERT: B 740 MET cc_start: 0.8584 (tmm) cc_final: 0.8281 (tmm) REVERT: C 369 MET cc_start: 0.8548 (ptm) cc_final: 0.8277 (ptt) REVERT: C 525 GLU cc_start: 0.8021 (pm20) cc_final: 0.7046 (mp0) REVERT: C 571 LEU cc_start: 0.8636 (mt) cc_final: 0.8411 (mt) REVERT: C 574 LYS cc_start: 0.8942 (ptmt) cc_final: 0.8640 (ptmt) REVERT: C 741 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7575 (tp-100) REVERT: C 798 MET cc_start: 0.7802 (pmm) cc_final: 0.7586 (pmm) REVERT: D 286 ASP cc_start: 0.7539 (t0) cc_final: 0.7319 (t0) REVERT: D 466 TRP cc_start: 0.6663 (p90) cc_final: 0.5744 (p90) REVERT: D 473 MET cc_start: 0.8507 (mmm) cc_final: 0.8271 (mmm) REVERT: D 546 CYS cc_start: 0.8261 (m) cc_final: 0.8053 (m) REVERT: D 580 GLU cc_start: 0.8701 (mp0) cc_final: 0.8363 (mp0) REVERT: D 740 MET cc_start: 0.8056 (tmm) cc_final: 0.7607 (tmm) REVERT: E 406 TYR cc_start: 0.7635 (m-10) cc_final: 0.7359 (m-10) REVERT: E 515 MET cc_start: 0.8765 (tpp) cc_final: 0.8202 (tpp) REVERT: E 626 LEU cc_start: 0.8877 (mm) cc_final: 0.8440 (mm) REVERT: E 777 MET cc_start: 0.7317 (mmp) cc_final: 0.6606 (mmt) REVERT: F 219 TRP cc_start: 0.6017 (t-100) cc_final: 0.5645 (t-100) REVERT: F 303 GLU cc_start: 0.6404 (mp0) cc_final: 0.5810 (mp0) REVERT: F 369 MET cc_start: 0.3259 (mpp) cc_final: 0.2878 (mpp) REVERT: F 371 MET cc_start: 0.7615 (tmm) cc_final: 0.7344 (tmm) REVERT: F 473 MET cc_start: 0.6678 (tmm) cc_final: 0.6320 (tmm) REVERT: F 515 MET cc_start: 0.8433 (ppp) cc_final: 0.7996 (ppp) REVERT: F 603 MET cc_start: 0.8314 (tpp) cc_final: 0.7944 (tpp) REVERT: F 646 ARG cc_start: 0.7864 (tpt170) cc_final: 0.7250 (tpp-160) REVERT: F 745 GLN cc_start: 0.8508 (mt0) cc_final: 0.8181 (mt0) outliers start: 2 outliers final: 0 residues processed: 400 average time/residue: 0.3434 time to fit residues: 224.7183 Evaluate side-chains 304 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 259 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN B 426 ASN B 459 HIS ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN D 412 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27242 Z= 0.223 Angle : 0.563 13.293 36900 Z= 0.282 Chirality : 0.041 0.248 4196 Planarity : 0.004 0.052 4790 Dihedral : 9.334 89.590 4024 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.92 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.65 (0.15), residues: 3397 helix: 1.53 (0.13), residues: 1756 sheet: -0.30 (0.27), residues: 367 loop : -0.86 (0.19), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 453 HIS 0.003 0.001 HIS A 459 PHE 0.023 0.002 PHE C 264 TYR 0.034 0.002 TYR D 752 ARG 0.004 0.000 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8648 (m-30) cc_final: 0.8038 (p0) REVERT: A 546 CYS cc_start: 0.8853 (m) cc_final: 0.8484 (m) REVERT: A 567 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8193 (mtpp) REVERT: A 576 VAL cc_start: 0.8235 (m) cc_final: 0.8005 (p) REVERT: A 772 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7362 (mp0) REVERT: B 319 GLU cc_start: 0.8051 (pm20) cc_final: 0.7817 (pm20) REVERT: B 546 CYS cc_start: 0.8799 (m) cc_final: 0.8327 (m) REVERT: B 603 MET cc_start: 0.7814 (mmp) cc_final: 0.7469 (tpp) REVERT: B 740 MET cc_start: 0.8585 (tmm) cc_final: 0.8284 (tmm) REVERT: C 369 MET cc_start: 0.8545 (ptm) cc_final: 0.8250 (ptt) REVERT: C 571 LEU cc_start: 0.8641 (mt) cc_final: 0.8395 (mt) REVERT: C 574 LYS cc_start: 0.8997 (ptmt) cc_final: 0.8703 (ptmt) REVERT: C 741 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7599 (tp-100) REVERT: D 231 MET cc_start: 0.6637 (tpp) cc_final: 0.6405 (tpt) REVERT: D 286 ASP cc_start: 0.7626 (t0) cc_final: 0.7400 (t0) REVERT: D 580 GLU cc_start: 0.8692 (mp0) cc_final: 0.8377 (mp0) REVERT: D 649 MET cc_start: 0.8115 (tpt) cc_final: 0.7823 (tpp) REVERT: D 740 MET cc_start: 0.8088 (tmm) cc_final: 0.7627 (tmm) REVERT: E 392 ASP cc_start: 0.7435 (m-30) cc_final: 0.7188 (m-30) REVERT: E 406 TYR cc_start: 0.7726 (m-10) cc_final: 0.7424 (m-10) REVERT: E 515 MET cc_start: 0.8762 (tpp) cc_final: 0.8212 (tpp) REVERT: E 626 LEU cc_start: 0.8897 (mm) cc_final: 0.8439 (mm) REVERT: E 777 MET cc_start: 0.7319 (mmp) cc_final: 0.6601 (mmt) REVERT: F 219 TRP cc_start: 0.6055 (t-100) cc_final: 0.5706 (t-100) REVERT: F 303 GLU cc_start: 0.6419 (mp0) cc_final: 0.5812 (mp0) REVERT: F 367 ILE cc_start: 0.7122 (mt) cc_final: 0.6843 (mt) REVERT: F 369 MET cc_start: 0.2819 (mpp) cc_final: 0.2498 (mpp) REVERT: F 371 MET cc_start: 0.7598 (tmm) cc_final: 0.7360 (tmm) REVERT: F 473 MET cc_start: 0.6759 (tmm) cc_final: 0.6456 (tmm) REVERT: F 603 MET cc_start: 0.8280 (tpp) cc_final: 0.7899 (tpp) REVERT: F 646 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7392 (tpp-160) REVERT: F 745 GLN cc_start: 0.8509 (mt0) cc_final: 0.8137 (mt0) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.3439 time to fit residues: 220.9291 Evaluate side-chains 301 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 7.9990 chunk 315 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 ASN B 459 HIS ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN D 412 GLN E 438 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27242 Z= 0.224 Angle : 0.563 11.585 36900 Z= 0.283 Chirality : 0.041 0.195 4196 Planarity : 0.005 0.102 4790 Dihedral : 9.311 89.264 4024 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.71 % Favored : 93.08 % Rotamer: Outliers : 0.04 % Allowed : 0.77 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.65 (0.15), residues: 3397 helix: 1.53 (0.13), residues: 1751 sheet: -0.29 (0.27), residues: 366 loop : -0.87 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 453 HIS 0.007 0.001 HIS E 438 PHE 0.029 0.002 PHE D 354 TYR 0.032 0.001 TYR D 752 ARG 0.008 0.000 ARG F 755 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8677 (m-30) cc_final: 0.8068 (p0) REVERT: A 515 MET cc_start: 0.8474 (ttm) cc_final: 0.7890 (tmm) REVERT: A 546 CYS cc_start: 0.8855 (m) cc_final: 0.8544 (m) REVERT: A 576 VAL cc_start: 0.8195 (m) cc_final: 0.7977 (p) REVERT: B 319 GLU cc_start: 0.8006 (pm20) cc_final: 0.7747 (pm20) REVERT: B 546 CYS cc_start: 0.8807 (m) cc_final: 0.8335 (m) REVERT: B 603 MET cc_start: 0.7780 (mmp) cc_final: 0.7351 (tpp) REVERT: B 740 MET cc_start: 0.8585 (tmm) cc_final: 0.8290 (tmm) REVERT: C 369 MET cc_start: 0.8530 (ptm) cc_final: 0.8214 (ptt) REVERT: C 473 MET cc_start: 0.7609 (ttt) cc_final: 0.7157 (tpp) REVERT: C 571 LEU cc_start: 0.8651 (mt) cc_final: 0.8418 (mt) REVERT: C 574 LYS cc_start: 0.8982 (ptmt) cc_final: 0.8697 (ptmt) REVERT: C 652 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7590 (mt-10) REVERT: C 741 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7614 (tp-100) REVERT: D 215 LEU cc_start: 0.8751 (tp) cc_final: 0.8520 (tp) REVERT: D 231 MET cc_start: 0.6640 (tpp) cc_final: 0.6397 (tpt) REVERT: D 281 GLU cc_start: 0.8943 (mp0) cc_final: 0.8628 (mp0) REVERT: D 286 ASP cc_start: 0.7623 (t0) cc_final: 0.7410 (t0) REVERT: D 473 MET cc_start: 0.8555 (mmm) cc_final: 0.8354 (mmm) REVERT: D 550 LEU cc_start: 0.9177 (tt) cc_final: 0.8945 (pp) REVERT: D 580 GLU cc_start: 0.8695 (mp0) cc_final: 0.8352 (mp0) REVERT: D 649 MET cc_start: 0.8059 (tpt) cc_final: 0.7738 (tpp) REVERT: D 740 MET cc_start: 0.8090 (tmm) cc_final: 0.7630 (tmm) REVERT: E 392 ASP cc_start: 0.7494 (m-30) cc_final: 0.7254 (m-30) REVERT: E 406 TYR cc_start: 0.7692 (m-10) cc_final: 0.7432 (m-10) REVERT: E 515 MET cc_start: 0.8764 (tpp) cc_final: 0.8219 (tpp) REVERT: E 626 LEU cc_start: 0.8910 (mm) cc_final: 0.8432 (mm) REVERT: E 777 MET cc_start: 0.7241 (mmp) cc_final: 0.6510 (mmt) REVERT: F 219 TRP cc_start: 0.6056 (t-100) cc_final: 0.5708 (t-100) REVERT: F 303 GLU cc_start: 0.6421 (mp0) cc_final: 0.5824 (mp0) REVERT: F 367 ILE cc_start: 0.7062 (mt) cc_final: 0.6806 (mt) REVERT: F 369 MET cc_start: 0.2898 (mpp) cc_final: 0.2537 (mpp) REVERT: F 371 MET cc_start: 0.7568 (tmm) cc_final: 0.7346 (tmm) REVERT: F 473 MET cc_start: 0.6764 (tmm) cc_final: 0.6476 (tmm) REVERT: F 603 MET cc_start: 0.8268 (tpp) cc_final: 0.7893 (tpp) REVERT: F 745 GLN cc_start: 0.8524 (mt0) cc_final: 0.8220 (mt0) outliers start: 1 outliers final: 0 residues processed: 395 average time/residue: 0.3524 time to fit residues: 228.0347 Evaluate side-chains 303 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 0.0970 chunk 324 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 225 optimal weight: 0.0050 chunk 340 optimal weight: 20.0000 chunk 313 optimal weight: 8.9990 chunk 271 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 209 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS B 426 ASN B 459 HIS ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27242 Z= 0.157 Angle : 0.548 12.299 36900 Z= 0.272 Chirality : 0.041 0.185 4196 Planarity : 0.004 0.072 4790 Dihedral : 9.137 87.390 4024 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.18 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.77 (0.15), residues: 3397 helix: 1.62 (0.13), residues: 1746 sheet: -0.22 (0.26), residues: 365 loop : -0.79 (0.19), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 453 HIS 0.008 0.001 HIS F 438 PHE 0.024 0.001 PHE C 264 TYR 0.014 0.001 TYR D 752 ARG 0.007 0.000 ARG D 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8677 (m-30) cc_final: 0.8046 (p0) REVERT: A 546 CYS cc_start: 0.8830 (m) cc_final: 0.8430 (m) REVERT: A 576 VAL cc_start: 0.8205 (m) cc_final: 0.8003 (p) REVERT: A 603 MET cc_start: 0.8852 (mmm) cc_final: 0.8439 (mmp) REVERT: A 772 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7348 (mm-30) REVERT: B 319 GLU cc_start: 0.7999 (pm20) cc_final: 0.7773 (pm20) REVERT: B 546 CYS cc_start: 0.8766 (m) cc_final: 0.8277 (m) REVERT: B 603 MET cc_start: 0.7611 (mmp) cc_final: 0.7188 (tpp) REVERT: B 740 MET cc_start: 0.8565 (tmm) cc_final: 0.8279 (tmm) REVERT: C 365 VAL cc_start: 0.9569 (t) cc_final: 0.9315 (m) REVERT: C 369 MET cc_start: 0.8544 (ptm) cc_final: 0.8257 (ptt) REVERT: C 473 MET cc_start: 0.7380 (ttt) cc_final: 0.7131 (tpp) REVERT: C 525 GLU cc_start: 0.8040 (pm20) cc_final: 0.6957 (mp0) REVERT: C 574 LYS cc_start: 0.8915 (ptmt) cc_final: 0.8633 (ptmt) REVERT: C 652 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7562 (mt-10) REVERT: C 741 GLN cc_start: 0.7802 (tp-100) cc_final: 0.7505 (tp-100) REVERT: D 231 MET cc_start: 0.6500 (tpp) cc_final: 0.6274 (tpt) REVERT: D 286 ASP cc_start: 0.7584 (t0) cc_final: 0.7355 (t0) REVERT: D 416 LYS cc_start: 0.8760 (tppt) cc_final: 0.8294 (tppt) REVERT: D 466 TRP cc_start: 0.6799 (p90) cc_final: 0.5912 (p90) REVERT: D 473 MET cc_start: 0.8523 (mmm) cc_final: 0.8313 (mmm) REVERT: D 550 LEU cc_start: 0.9141 (tt) cc_final: 0.8906 (pp) REVERT: D 580 GLU cc_start: 0.8634 (mp0) cc_final: 0.8349 (mp0) REVERT: D 649 MET cc_start: 0.7931 (tpt) cc_final: 0.7675 (tpp) REVERT: D 740 MET cc_start: 0.8118 (tmm) cc_final: 0.7786 (tmm) REVERT: E 297 CYS cc_start: 0.8268 (p) cc_final: 0.8026 (t) REVERT: E 304 ILE cc_start: 0.9331 (tp) cc_final: 0.9108 (tp) REVERT: E 392 ASP cc_start: 0.7547 (m-30) cc_final: 0.7310 (m-30) REVERT: E 406 TYR cc_start: 0.7648 (m-10) cc_final: 0.7365 (m-10) REVERT: E 515 MET cc_start: 0.8711 (tpp) cc_final: 0.8218 (tpp) REVERT: E 626 LEU cc_start: 0.8869 (mm) cc_final: 0.8378 (mm) REVERT: E 777 MET cc_start: 0.7189 (mmp) cc_final: 0.6596 (mmt) REVERT: F 303 GLU cc_start: 0.6396 (mp0) cc_final: 0.5807 (mp0) REVERT: F 603 MET cc_start: 0.8227 (tpp) cc_final: 0.7806 (tpp) REVERT: F 745 GLN cc_start: 0.8505 (mt0) cc_final: 0.8191 (mt0) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.3334 time to fit residues: 218.8513 Evaluate side-chains 311 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 7.9990 chunk 289 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 271 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 279 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 ASN B 426 ASN B 459 HIS ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 ASN D 350 ASN D 412 GLN E 438 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.098316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.077583 restraints weight = 70801.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.079591 restraints weight = 43511.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.080973 restraints weight = 30616.362| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27242 Z= 0.222 Angle : 0.565 11.639 36900 Z= 0.283 Chirality : 0.041 0.191 4196 Planarity : 0.005 0.100 4790 Dihedral : 9.176 87.409 4024 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.04 % Favored : 92.76 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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 (0.15), residues: 3397 helix: 1.58 (0.13), residues: 1761 sheet: -0.27 (0.26), residues: 369 loop : -0.84 (0.19), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 219 HIS 0.008 0.001 HIS E 438 PHE 0.025 0.002 PHE D 731 TYR 0.030 0.001 TYR D 752 ARG 0.007 0.000 ARG D 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5045.59 seconds wall clock time: 92 minutes 11.24 seconds (5531.24 seconds total)