Starting phenix.real_space_refine on Tue Feb 20 09:41:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vnw_21251/02_2024/6vnw_21251.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vnw_21251/02_2024/6vnw_21251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vnw_21251/02_2024/6vnw_21251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vnw_21251/02_2024/6vnw_21251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vnw_21251/02_2024/6vnw_21251.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vnw_21251/02_2024/6vnw_21251.pdb" } resolution = 3.44 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 17361 2.51 5 N 4848 2.21 5 O 5163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ASP 22": "OD1" <-> "OD2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 562": "OD1" <-> "OD2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 686": "NH1" <-> "NH2" Residue "B ARG 699": "NH1" <-> "NH2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "E TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "E PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 416": "OE1" <-> "OE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ASP 12": "OD1" <-> "OD2" Residue "G ARG 25": "NH1" <-> "NH2" Residue "G ASP 46": "OD1" <-> "OD2" Residue "G ARG 56": "NH1" <-> "NH2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 119": "NH1" <-> "NH2" Residue "G TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "G ARG 207": "NH1" <-> "NH2" Residue "G PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G ASP 297": "OD1" <-> "OD2" Residue "G TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C ASP 676": "OD1" <-> "OD2" Residue "C PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 680": "OD1" <-> "OD2" Residue "C ASP 701": "OD1" <-> "OD2" Residue "C ASP 704": "OD1" <-> "OD2" Residue "C ASP 713": "OD1" <-> "OD2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 223": "NH1" <-> "NH2" Residue "F ARG 228": "NH1" <-> "NH2" Residue "F PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 277": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F ASP 326": "OD1" <-> "OD2" Residue "F ARG 333": "NH1" <-> "NH2" Residue "F PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 337": "NH1" <-> "NH2" Residue "F PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 371": "NH1" <-> "NH2" Residue "F TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 462": "OD1" <-> "OD2" Residue "F GLU 478": "OE1" <-> "OE2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 7": "NH1" <-> "NH2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 66": "OE1" <-> "OE2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 149": "NH1" <-> "NH2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I ARG 173": "NH1" <-> "NH2" Residue "I ARG 189": "NH1" <-> "NH2" Residue "I PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 284": "OD1" <-> "OD2" Residue "I TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 298": "OE1" <-> "OE2" Residue "I ASP 351": "OD1" <-> "OD2" Residue "I TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 362": "OD1" <-> "OD2" Residue "I PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 499": "OE1" <-> "OE2" Residue "I PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 528": "NH1" <-> "NH2" Residue "I PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 600": "NH1" <-> "NH2" Residue "I PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 608": "OD1" <-> "OD2" Residue "I GLU 615": "OE1" <-> "OE2" Residue "I GLU 622": "OE1" <-> "OE2" Residue "I TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 647": "OE1" <-> "OE2" Residue "I ASP 650": "OD1" <-> "OD2" Residue "I ARG 656": "NH1" <-> "NH2" Residue "I GLU 660": "OE1" <-> "OE2" Residue "I GLU 664": "OE1" <-> "OE2" Residue "I ARG 669": "NH1" <-> "NH2" Residue "I ARG 679": "NH1" <-> "NH2" Residue "I TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 715": "OE1" <-> "OE2" Residue "I PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 765": "OE1" <-> "OE2" Residue "I ASP 804": "OD1" <-> "OD2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "D ASP 258": "OD1" <-> "OD2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 385": "OD1" <-> "OD2" Residue "D ARG 429": "NH1" <-> "NH2" Residue "D ASP 436": "OD1" <-> "OD2" Residue "D ARG 440": "NH1" <-> "NH2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 532": "NH1" <-> "NH2" Residue "D PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 588": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27486 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 421 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "B" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 3957 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 361} Link IDs: {'PTRANS': 22, 'TRANS': 636} Chain breaks: 4 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1256 Unresolved non-hydrogen angles: 1625 Unresolved non-hydrogen dihedrals: 1031 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 15, 'TYR:plan': 14, 'ASN:plan1': 21, 'TRP:plan': 3, 'ASP:plan': 26, 'PHE:plan': 18, 'GLU:plan': 23, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 684 Chain: "E" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3107 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2411 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "C" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 3666 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 482} Link IDs: {'PTRANS': 25, 'TRANS': 639} Chain breaks: 8 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1679 Unresolved non-hydrogen angles: 2149 Unresolved non-hydrogen dihedrals: 1378 Unresolved non-hydrogen chiralities: 163 Planarities with less than four sites: {'GLN:plan1': 30, 'ASP:plan': 34, 'TYR:plan': 19, 'ASN:plan1': 21, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 22, 'GLU:plan': 35, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 902 Chain: "F" Number of atoms: 3797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3797 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 20, 'TRANS': 454} Chain breaks: 2 Chain: "I" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6034 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 31, 'TRANS': 732} Chain breaks: 5 Chain: "D" Number of atoms: 4093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4093 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 33, 'TRANS': 494} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 13.51, per 1000 atoms: 0.49 Number of scatterers: 27486 At special positions: 0 Unit cell: (124.8, 146.9, 205.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5163 8.00 N 4848 7.00 C 17361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.74 Conformation dependent library (CDL) restraints added in 5.7 seconds 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7214 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 46 sheets defined 36.2% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'H' and resid 38 through 58 removed outlier: 3.671A pdb=" N GLU H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 339 through 359 removed outlier: 3.552A pdb=" N GLN B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 removed outlier: 3.970A pdb=" N GLU B 494 " --> pdb=" O PRO B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 586 through 634 removed outlier: 3.548A pdb=" N GLU B 592 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 685 Processing helix chain 'B' and resid 689 through 704 removed outlier: 3.525A pdb=" N GLN B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.832A pdb=" N ILE E 44 " --> pdb=" O HIS E 40 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 49 through 63 removed outlier: 3.608A pdb=" N ILE E 55 " --> pdb=" O CYS E 51 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN E 60 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.677A pdb=" N LEU E 104 " --> pdb=" O CYS E 100 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.752A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 148 removed outlier: 4.273A pdb=" N CYS E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 165 Processing helix chain 'E' and resid 167 through 182 Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.765A pdb=" N ALA E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 218 through 232 removed outlier: 3.667A pdb=" N TYR E 231 " --> pdb=" O ASN E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 249 removed outlier: 3.979A pdb=" N ALA E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 263 removed outlier: 3.790A pdb=" N ALA E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 283 Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.904A pdb=" N CYS E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 Processing helix chain 'E' and resid 321 through 334 removed outlier: 3.900A pdb=" N HIS E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 349 Processing helix chain 'E' and resid 353 through 368 removed outlier: 3.574A pdb=" N ALA E 357 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 385 removed outlier: 4.362A pdb=" N ASN E 375 " --> pdb=" O ASN E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 402 removed outlier: 3.746A pdb=" N ALA E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 423 removed outlier: 3.788A pdb=" N GLU E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 133 removed outlier: 3.806A pdb=" N SER G 123 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 260 removed outlier: 4.225A pdb=" N LEU G 243 " --> pdb=" O PRO G 239 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN G 260 " --> pdb=" O VAL G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'C' and resid 336 through 367 Processing helix chain 'C' and resid 516 through 528 Processing helix chain 'C' and resid 569 through 587 removed outlier: 3.758A pdb=" N ILE C 573 " --> pdb=" O ASN C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 634 Proline residue: C 611 - end of helix removed outlier: 3.869A pdb=" N LEU C 625 " --> pdb=" O LYS C 621 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP C 627 " --> pdb=" O VAL C 623 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.918A pdb=" N ASN C 638 " --> pdb=" O HIS C 635 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 639 " --> pdb=" O GLU C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 639' Processing helix chain 'C' and resid 643 through 661 removed outlier: 3.813A pdb=" N ILE C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C 651 " --> pdb=" O ARG C 647 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 652 " --> pdb=" O CYS C 648 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 661 " --> pdb=" O GLN C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 684 removed outlier: 3.615A pdb=" N HIS C 666 " --> pdb=" O LYS C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 704 through 715 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 17 through 30 removed outlier: 3.616A pdb=" N GLN F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 48 removed outlier: 3.607A pdb=" N TRP F 37 " --> pdb=" O ASP F 33 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.604A pdb=" N ASP F 54 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 removed outlier: 4.153A pdb=" N GLU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 167 through 172 removed outlier: 3.503A pdb=" N TYR F 171 " --> pdb=" O ASN F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 188 removed outlier: 4.264A pdb=" N ALA F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.651A pdb=" N LYS F 214 " --> pdb=" O ASP F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 removed outlier: 3.927A pdb=" N GLN F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 277 through 291 removed outlier: 3.543A pdb=" N LEU F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 308 removed outlier: 3.648A pdb=" N ALA F 297 " --> pdb=" O ASN F 293 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 325 Processing helix chain 'F' and resid 327 through 341 removed outlier: 3.690A pdb=" N LEU F 338 " --> pdb=" O PHE F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 359 removed outlier: 3.971A pdb=" N PHE F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 376 removed outlier: 3.502A pdb=" N PHE F 369 " --> pdb=" O THR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 397 Processing helix chain 'F' and resid 398 through 413 removed outlier: 3.747A pdb=" N ALA F 402 " --> pdb=" O ASP F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 431 Processing helix chain 'F' and resid 432 through 447 Processing helix chain 'F' and resid 451 through 465 Processing helix chain 'F' and resid 466 through 481 removed outlier: 3.734A pdb=" N LYS F 476 " --> pdb=" O ALA F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 498 Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 207 through 213 Processing helix chain 'I' and resid 377 through 396 removed outlier: 3.524A pdb=" N ASN I 396 " --> pdb=" O ILE I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 530 through 533 Processing helix chain 'I' and resid 558 through 563 Processing helix chain 'I' and resid 605 through 627 removed outlier: 3.682A pdb=" N LEU I 609 " --> pdb=" O GLN I 605 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP I 610 " --> pdb=" O PHE I 606 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU I 611 " --> pdb=" O GLU I 607 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE I 612 " --> pdb=" O ASP I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 686 removed outlier: 3.537A pdb=" N ILE I 649 " --> pdb=" O TYR I 645 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 668 " --> pdb=" O GLU I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 694 through 742 Processing helix chain 'I' and resid 745 through 757 Processing helix chain 'I' and resid 767 through 783 Processing helix chain 'I' and resid 787 through 794 Processing helix chain 'I' and resid 805 through 821 Processing helix chain 'D' and resid 132 through 137 removed outlier: 3.803A pdb=" N ASP D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.896A pdb=" N GLN D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 removed outlier: 4.059A pdb=" N LYS D 153 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 removed outlier: 3.575A pdb=" N HIS D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.568A pdb=" N VAL D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 474 removed outlier: 3.557A pdb=" N MET D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 289 through 293 removed outlier: 4.768A pdb=" N GLU B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN D 365 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 357 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 367 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.890A pdb=" N LYS B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 81 removed outlier: 3.990A pdb=" N PHE B 112 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP B 104 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 110 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.962A pdb=" N PHE B 155 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 169 removed outlier: 3.924A pdb=" N SER B 165 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 188 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU B 199 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 190 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.942A pdb=" N SER B 208 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP B 236 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 250 removed outlier: 3.551A pdb=" N SER B 246 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA9, first strand: chain 'B' and resid 383 through 390 Processing sheet with id=AB1, first strand: chain 'B' and resid 427 through 430 removed outlier: 4.423A pdb=" N ILE B 417 " --> pdb=" O HIS B 428 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 415 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 412 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY B 462 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 414 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 458 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR C 480 " --> pdb=" O PRO C 474 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN C 469 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE C 409 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR C 471 " --> pdb=" O VAL C 407 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL C 407 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 473 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 427 through 430 removed outlier: 4.423A pdb=" N ILE B 417 " --> pdb=" O HIS B 428 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 415 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 412 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY B 462 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 414 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 458 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 531 through 536 Processing sheet with id=AB4, first strand: chain 'G' and resid 13 through 15 removed outlier: 3.520A pdb=" N ASP G 32 " --> pdb=" O VAL G 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 37 through 40 removed outlier: 6.233A pdb=" N ALA G 94 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR G 81 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR G 96 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE G 79 " --> pdb=" O TYR G 96 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU G 98 " --> pdb=" O LEU G 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 141 through 142 removed outlier: 3.730A pdb=" N LYS G 141 " --> pdb=" O SER G 200 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG G 186 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY G 178 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN G 165 " --> pdb=" O GLY G 178 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE G 180 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS G 163 " --> pdb=" O PHE G 180 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 182 " --> pdb=" O TYR G 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 206 through 210 removed outlier: 6.884A pdb=" N GLU G 223 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL G 209 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL G 221 " --> pdb=" O VAL G 209 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 314 through 316 Processing sheet with id=AB9, first strand: chain 'C' and resid 6 through 12 removed outlier: 4.968A pdb=" N ILE C 314 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 306 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE C 292 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER C 308 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 21 through 24 removed outlier: 3.799A pdb=" N LYS C 34 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 69 through 72 removed outlier: 3.653A pdb=" N LEU C 101 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 114 through 117 removed outlier: 6.263A pdb=" N CYS C 133 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 147 through 152 removed outlier: 4.115A pdb=" N ASP C 149 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 171 " --> pdb=" O CYS C 167 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 182 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLN C 176 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 190 through 193 Processing sheet with id=AC6, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC7, first strand: chain 'C' and resid 244 through 247 removed outlier: 6.346A pdb=" N VAL C 266 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP C 282 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 268 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 384 through 387 removed outlier: 4.261A pdb=" N THR C 386 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 510 through 512 removed outlier: 3.779A pdb=" N GLU C 562 " --> pdb=" O ARG C 559 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 6 through 13 removed outlier: 4.980A pdb=" N ASP I 8 " --> pdb=" O TYR I 358 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR I 358 " --> pdb=" O ASP I 8 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TRP I 10 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU I 348 " --> pdb=" O ALA I 332 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA I 332 " --> pdb=" O LEU I 348 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 26 through 28 removed outlier: 3.574A pdb=" N ALA I 28 " --> pdb=" O LYS I 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 79 through 84 removed outlier: 4.766A pdb=" N GLN I 80 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU I 98 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU I 95 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR I 127 " --> pdb=" O VAL I 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 108 through 111 Processing sheet with id=AD5, first strand: chain 'I' and resid 138 through 141 Processing sheet with id=AD6, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AD7, first strand: chain 'I' and resid 245 through 251 removed outlier: 7.193A pdb=" N LEU I 263 " --> pdb=" O ILE I 246 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE I 248 " --> pdb=" O PHE I 261 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE I 261 " --> pdb=" O ILE I 248 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE I 250 " --> pdb=" O SER I 259 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER I 259 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 287 through 291 removed outlier: 3.765A pdb=" N CYS I 289 " --> pdb=" O GLY I 306 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU I 312 " --> pdb=" O ALA I 323 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA I 323 " --> pdb=" O LEU I 312 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE I 314 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR I 319 " --> pdb=" O GLN I 316 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 411 through 417 Processing sheet with id=AE1, first strand: chain 'I' and resid 471 through 474 removed outlier: 5.573A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER I 509 " --> pdb=" O LYS I 454 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 535 through 537 Processing sheet with id=AE3, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AE4, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 202 removed outlier: 3.706A pdb=" N ALA D 240 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASP D 232 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE D 238 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 272 through 273 Processing sheet with id=AE7, first strand: chain 'D' and resid 295 through 297 removed outlier: 3.749A pdb=" N VAL D 296 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 303 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU D 311 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR D 323 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY D 313 " --> pdb=" O LEU D 321 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 390 through 391 Processing sheet with id=AE9, first strand: chain 'D' and resid 487 through 493 Processing sheet with id=AF1, first strand: chain 'D' and resid 534 through 536 1414 hydrogen bonds defined for protein. 4053 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: 11.79 Time building geometry restraints manager: 11.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4824 1.32 - 1.44: 6800 1.44 - 1.57: 16118 1.57 - 1.69: 0 1.69 - 1.82: 175 Bond restraints: 27917 Sorted by residual: bond pdb=" CA ALA B 167 " pdb=" CB ALA B 167 " ideal model delta sigma weight residual 1.534 1.474 0.060 1.76e-02 3.23e+03 1.15e+01 bond pdb=" CA SER I 364 " pdb=" CB SER I 364 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.52e-02 4.33e+03 1.08e+01 bond pdb=" N SER E 410 " pdb=" CA SER E 410 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.28e-02 6.10e+03 1.05e+01 bond pdb=" C PRO I 363 " pdb=" O PRO I 363 " ideal model delta sigma weight residual 1.233 1.196 0.037 1.16e-02 7.43e+03 1.01e+01 bond pdb=" N VAL B 257 " pdb=" CA VAL B 257 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.67e+00 ... (remaining 27912 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.40: 673 106.40 - 113.35: 15278 113.35 - 120.30: 10143 120.30 - 127.25: 11624 127.25 - 134.20: 218 Bond angle restraints: 37936 Sorted by residual: angle pdb=" C ASP B 172 " pdb=" CA ASP B 172 " pdb=" CB ASP B 172 " ideal model delta sigma weight residual 109.83 118.14 -8.31 9.90e-01 1.02e+00 7.05e+01 angle pdb=" N THR B 487 " pdb=" CA THR B 487 " pdb=" C THR B 487 " ideal model delta sigma weight residual 108.07 116.75 -8.68 1.38e+00 5.25e-01 3.95e+01 angle pdb=" N HIS E 40 " pdb=" CA HIS E 40 " pdb=" C HIS E 40 " ideal model delta sigma weight residual 114.09 105.07 9.02 1.55e+00 4.16e-01 3.38e+01 angle pdb=" C ASP B 251 " pdb=" CA ASP B 251 " pdb=" CB ASP B 251 " ideal model delta sigma weight residual 111.70 103.14 8.56 1.48e+00 4.57e-01 3.34e+01 angle pdb=" N GLN F 17 " pdb=" CA GLN F 17 " pdb=" C GLN F 17 " ideal model delta sigma weight residual 112.72 105.67 7.05 1.28e+00 6.10e-01 3.03e+01 ... (remaining 37931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 15104 17.71 - 35.41: 1372 35.41 - 53.12: 252 53.12 - 70.82: 49 70.82 - 88.53: 26 Dihedral angle restraints: 16803 sinusoidal: 5682 harmonic: 11121 Sorted by residual: dihedral pdb=" C ASP B 172 " pdb=" N ASP B 172 " pdb=" CA ASP B 172 " pdb=" CB ASP B 172 " ideal model delta harmonic sigma weight residual -122.60 -137.29 14.69 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" CA GLY D 50 " pdb=" C GLY D 50 " pdb=" N GLU D 51 " pdb=" CA GLU D 51 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA THR G 40 " pdb=" C THR G 40 " pdb=" N LYS G 41 " pdb=" CA LYS G 41 " ideal model delta harmonic sigma weight residual 180.00 -151.20 -28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 16800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4125 0.096 - 0.193: 297 0.193 - 0.289: 28 0.289 - 0.385: 11 0.385 - 0.481: 3 Chirality restraints: 4464 Sorted by residual: chirality pdb=" CA ASP B 172 " pdb=" N ASP B 172 " pdb=" C ASP B 172 " pdb=" CB ASP B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CA PHE B 171 " pdb=" N PHE B 171 " pdb=" C PHE B 171 " pdb=" CB PHE B 171 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA GLU B 259 " pdb=" N GLU B 259 " pdb=" C GLU B 259 " pdb=" CB GLU B 259 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 4461 not shown) Planarity restraints: 4968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 16 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C PHE F 16 " -0.058 2.00e-02 2.50e+03 pdb=" O PHE F 16 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN F 17 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 250 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C PHE B 250 " -0.055 2.00e-02 2.50e+03 pdb=" O PHE B 250 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 251 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 347 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C ALA E 347 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA E 347 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU E 348 " -0.017 2.00e-02 2.50e+03 ... (remaining 4965 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 370 2.64 - 3.21: 24762 3.21 - 3.77: 40946 3.77 - 4.34: 55101 4.34 - 4.90: 91776 Nonbonded interactions: 212955 Sorted by model distance: nonbonded pdb=" O HIS E 40 " pdb=" ND1 HIS E 40 " model vdw 2.078 2.520 nonbonded pdb=" OE1 GLU F 2 " pdb=" OG1 THR I 134 " model vdw 2.202 2.440 nonbonded pdb=" CZ PHE I 724 " pdb=" O LEU I 759 " model vdw 2.205 3.340 nonbonded pdb=" OG1 THR G 83 " pdb=" OE1 GLU G 93 " model vdw 2.208 2.440 nonbonded pdb=" N LEU G 88 " pdb=" OE2 GLU F 379 " model vdw 2.222 2.520 ... (remaining 212950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 7.990 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 71.850 Find NCS groups from input model: 0.990 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 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 : 0.004 0.065 27917 Z= 0.295 Angle : 0.806 9.608 37936 Z= 0.483 Chirality : 0.055 0.481 4464 Planarity : 0.004 0.062 4968 Dihedral : 14.769 88.528 9589 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.12 % Favored : 91.74 % Rotamer: Outliers : 2.05 % Allowed : 6.87 % Favored : 91.08 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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: -3.20 (0.12), residues: 3767 helix: -0.54 (0.13), residues: 1287 sheet: -2.28 (0.16), residues: 836 loop : -3.37 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 237 HIS 0.011 0.001 HIS D 74 PHE 0.019 0.002 PHE D 46 TYR 0.023 0.002 TYR E 43 ARG 0.008 0.000 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 690 time to evaluate : 3.017 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 LYS cc_start: 0.7672 (mtpt) cc_final: 0.7445 (mmtt) REVERT: B 555 THR cc_start: 0.5727 (m) cc_final: 0.5380 (m) REVERT: B 629 GLU cc_start: 0.7491 (tp30) cc_final: 0.7243 (mm-30) REVERT: B 660 ILE cc_start: 0.8300 (tp) cc_final: 0.8059 (mt) REVERT: B 684 HIS cc_start: 0.8044 (t70) cc_final: 0.7812 (t-90) REVERT: E 57 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: E 61 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5516 (tt0) REVERT: E 361 TYR cc_start: 0.6035 (m-80) cc_final: 0.5808 (m-80) REVERT: E 414 ASP cc_start: 0.5145 (m-30) cc_final: 0.4636 (m-30) REVERT: G 9 GLU cc_start: 0.7722 (mp0) cc_final: 0.7508 (mp0) REVERT: G 249 GLU cc_start: 0.7736 (pp20) cc_final: 0.7404 (pp20) REVERT: C 622 LYS cc_start: 0.7831 (mttt) cc_final: 0.7284 (mttt) REVERT: C 648 CYS cc_start: 0.7043 (m) cc_final: 0.6520 (p) REVERT: C 681 LYS cc_start: 0.6082 (pptt) cc_final: 0.5742 (mttt) REVERT: F 22 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6410 (tt) REVERT: F 79 SER cc_start: 0.8141 (t) cc_final: 0.7893 (p) REVERT: F 326 ASP cc_start: 0.8014 (p0) cc_final: 0.7581 (t0) REVERT: I 285 TYR cc_start: 0.8651 (p90) cc_final: 0.8407 (p90) REVERT: I 301 ILE cc_start: 0.8162 (mt) cc_final: 0.7754 (mt) REVERT: I 325 GLN cc_start: 0.8187 (tt0) cc_final: 0.7934 (tt0) outliers start: 51 outliers final: 16 residues processed: 729 average time/residue: 0.4030 time to fit residues: 454.5416 Evaluate side-chains 446 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 427 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 225 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 320 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 153 optimal weight: 50.0000 chunk 297 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 180 optimal weight: 50.0000 chunk 221 optimal weight: 1.9990 chunk 344 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN B 651 ASN B 705 ASN E 91 GLN E 99 GLN E 106 GLN E 224 HIS ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 ASN G 60 HIS G 74 ASN G 78 ASN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN G 176 ASN G 190 HIS G 194 ASN G 205 GLN G 251 ASN G 334 GLN C 610 HIS ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 188 HIS ** F 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN F 307 GLN F 322 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 ASN F 360 GLN ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 HIS ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 456 ASN F 496 GLN I 22 GLN I 73 HIS I 120 GLN I 200 HIS I 201 GLN I 420 ASN ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 651 HIS I 677 GLN I 693 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS D 97 HIS D 197 GLN D 225 ASN D 291 GLN D 449 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 27917 Z= 0.502 Angle : 0.798 10.615 37936 Z= 0.412 Chirality : 0.050 0.206 4464 Planarity : 0.005 0.058 4968 Dihedral : 6.462 103.251 4075 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.99 % Favored : 91.93 % Rotamer: Outliers : 4.02 % Allowed : 16.35 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.13), residues: 3767 helix: 0.37 (0.14), residues: 1328 sheet: -1.98 (0.17), residues: 843 loop : -2.99 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 9 HIS 0.021 0.002 HIS E 249 PHE 0.029 0.003 PHE I 45 TYR 0.028 0.003 TYR C 660 ARG 0.009 0.001 ARG D 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 408 time to evaluate : 3.034 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: H 7 MET cc_start: 0.7716 (tmm) cc_final: 0.7215 (tmm) REVERT: B 603 TYR cc_start: 0.7544 (m-80) cc_final: 0.7260 (m-80) REVERT: E 285 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8078 (ttmt) REVERT: E 417 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5554 (ptt) REVERT: G 82 ARG cc_start: 0.7065 (tpp-160) cc_final: 0.6763 (tpp-160) REVERT: G 129 ARG cc_start: 0.7607 (tpm170) cc_final: 0.7142 (ttp-110) REVERT: G 132 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7864 (pt0) REVERT: G 249 GLU cc_start: 0.7845 (pp20) cc_final: 0.7388 (pp20) REVERT: C 648 CYS cc_start: 0.7235 (m) cc_final: 0.7035 (m) REVERT: C 657 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7541 (mm-40) REVERT: F 60 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8133 (tp) REVERT: F 326 ASP cc_start: 0.7877 (p0) cc_final: 0.7403 (t0) REVERT: I 16 ASP cc_start: 0.7028 (p0) cc_final: 0.6756 (p0) REVERT: I 205 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: I 456 LYS cc_start: 0.7487 (mmmt) cc_final: 0.7239 (ttpt) REVERT: D 94 MET cc_start: 0.3908 (ttt) cc_final: 0.3217 (tpt) REVERT: D 307 ASN cc_start: 0.7765 (t0) cc_final: 0.7544 (t0) outliers start: 100 outliers final: 55 residues processed: 480 average time/residue: 0.3765 time to fit residues: 290.0101 Evaluate side-chains 415 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 357 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 194 ASN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 712 PHE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 205 TYR Chi-restraints excluded: chain I residue 249 CYS Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 507 SER Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 665 LEU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 744 LEU Chi-restraints excluded: chain I residue 765 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 191 optimal weight: 50.0000 chunk 106 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 344 optimal weight: 40.0000 chunk 372 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 341 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 276 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 ASN G 307 ASN ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 216 GLN F 233 GLN F 265 ASN F 422 ASN ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 488 GLN I 37 GLN I 155 GLN I 420 ASN ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 576 ASN I 694 HIS ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27917 Z= 0.221 Angle : 0.621 15.561 37936 Z= 0.320 Chirality : 0.044 0.183 4464 Planarity : 0.004 0.057 4968 Dihedral : 5.064 59.684 4043 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 3.69 % Allowed : 19.48 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3767 helix: 1.24 (0.14), residues: 1311 sheet: -1.69 (0.17), residues: 849 loop : -2.60 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 9 HIS 0.016 0.001 HIS E 249 PHE 0.027 0.002 PHE B 501 TYR 0.024 0.002 TYR E 191 ARG 0.005 0.000 ARG F 430 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 403 time to evaluate : 3.423 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 MET cc_start: 0.7938 (tmm) cc_final: 0.7363 (tmm) REVERT: E 254 VAL cc_start: 0.6886 (OUTLIER) cc_final: 0.6643 (t) REVERT: G 32 ASP cc_start: 0.7103 (m-30) cc_final: 0.6851 (m-30) REVERT: G 34 LEU cc_start: 0.8669 (tp) cc_final: 0.8390 (tt) REVERT: G 82 ARG cc_start: 0.6812 (tpp-160) cc_final: 0.6468 (tpp-160) REVERT: G 249 GLU cc_start: 0.7896 (pp20) cc_final: 0.7277 (pp20) REVERT: C 670 LEU cc_start: 0.5928 (mp) cc_final: 0.5519 (mt) REVERT: F 46 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7359 (mm-30) REVERT: F 193 LYS cc_start: 0.7719 (mtmt) cc_final: 0.7236 (mttt) REVERT: F 326 ASP cc_start: 0.7798 (p0) cc_final: 0.7219 (t0) REVERT: I 16 ASP cc_start: 0.6884 (p0) cc_final: 0.6522 (p0) REVERT: I 76 ASP cc_start: 0.7894 (p0) cc_final: 0.7640 (p0) REVERT: I 309 ASN cc_start: 0.8221 (t0) cc_final: 0.7752 (t0) REVERT: I 389 GLN cc_start: 0.7397 (tt0) cc_final: 0.6611 (tm-30) REVERT: D 94 MET cc_start: 0.3669 (ttt) cc_final: 0.3130 (tpt) REVERT: D 274 ILE cc_start: 0.3785 (OUTLIER) cc_final: 0.3359 (mt) REVERT: D 307 ASN cc_start: 0.7758 (t0) cc_final: 0.7496 (t0) REVERT: D 590 LEU cc_start: 0.4816 (OUTLIER) cc_final: 0.4467 (pp) outliers start: 92 outliers final: 44 residues processed: 470 average time/residue: 0.3743 time to fit residues: 284.5189 Evaluate side-chains 402 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 355 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 744 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 590 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 340 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 chunk 38 optimal weight: 50.0000 chunk 164 optimal weight: 8.9990 chunk 231 optimal weight: 0.9980 chunk 346 optimal weight: 8.9990 chunk 366 optimal weight: 1.9990 chunk 180 optimal weight: 30.0000 chunk 327 optimal weight: 7.9990 chunk 98 optimal weight: 0.0870 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 642 ASN B 664 ASN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN E 117 HIS E 139 HIS ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 HIS I 353 HIS ** I 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 448 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 778 HIS ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.112 27917 Z= 0.653 Angle : 0.851 11.650 37936 Z= 0.438 Chirality : 0.053 0.225 4464 Planarity : 0.005 0.055 4968 Dihedral : 5.667 56.504 4041 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.95 % Favored : 90.95 % Rotamer: Outliers : 5.50 % Allowed : 20.64 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 3767 helix: 0.58 (0.14), residues: 1317 sheet: -1.80 (0.17), residues: 850 loop : -2.66 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 237 HIS 0.018 0.003 HIS E 314 PHE 0.036 0.003 PHE I 45 TYR 0.032 0.003 TYR F 300 ARG 0.009 0.001 ARG F 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 385 time to evaluate : 2.796 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 MET cc_start: 0.7758 (tmm) cc_final: 0.7070 (tmm) REVERT: E 232 ASP cc_start: 0.6749 (t0) cc_final: 0.6404 (t0) REVERT: E 235 ASN cc_start: 0.7342 (t0) cc_final: 0.6891 (t0) REVERT: E 245 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6701 (ptp) REVERT: E 254 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7872 (t) REVERT: G 34 LEU cc_start: 0.8825 (tp) cc_final: 0.8531 (tt) REVERT: G 49 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7594 (ttm-80) REVERT: G 82 ARG cc_start: 0.6962 (tpp-160) cc_final: 0.6614 (tpp-160) REVERT: G 168 TRP cc_start: 0.8440 (m-90) cc_final: 0.8164 (m-90) REVERT: G 249 GLU cc_start: 0.8144 (pp20) cc_final: 0.7559 (pp20) REVERT: C 626 ILE cc_start: 0.8915 (tp) cc_final: 0.8399 (tt) REVERT: C 670 LEU cc_start: 0.6120 (mp) cc_final: 0.5910 (mt) REVERT: F 265 ASN cc_start: 0.8064 (m110) cc_final: 0.7633 (m110) REVERT: I 16 ASP cc_start: 0.7183 (p0) cc_final: 0.6779 (p0) REVERT: I 205 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: I 271 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7830 (mt) REVERT: I 290 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8903 (p90) REVERT: I 733 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8548 (tp) REVERT: D 94 MET cc_start: 0.4036 (ttt) cc_final: 0.3073 (tpt) REVERT: D 274 ILE cc_start: 0.3829 (OUTLIER) cc_final: 0.3325 (mt) REVERT: D 307 ASN cc_start: 0.7886 (t0) cc_final: 0.7631 (t0) REVERT: D 488 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8345 (tt) REVERT: D 583 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8180 (t0) REVERT: D 584 MET cc_start: 0.8944 (tpp) cc_final: 0.8715 (mmm) outliers start: 137 outliers final: 85 residues processed: 488 average time/residue: 0.3638 time to fit residues: 284.1684 Evaluate side-chains 426 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 332 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 205 TYR Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 601 ILE Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 744 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 590 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 305 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 272 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 312 optimal weight: 0.6980 chunk 253 optimal weight: 0.0270 chunk 0 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 328 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 642 ASN E 99 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 456 ASN I 377 ASN I 420 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27917 Z= 0.204 Angle : 0.617 11.227 37936 Z= 0.318 Chirality : 0.044 0.245 4464 Planarity : 0.004 0.050 4968 Dihedral : 5.040 56.452 4041 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.53 % Favored : 93.42 % Rotamer: Outliers : 4.02 % Allowed : 22.69 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3767 helix: 1.42 (0.14), residues: 1313 sheet: -1.52 (0.17), residues: 850 loop : -2.41 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 9 HIS 0.012 0.001 HIS E 249 PHE 0.021 0.002 PHE B 501 TYR 0.026 0.001 TYR G 137 ARG 0.004 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 379 time to evaluate : 3.251 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: symmetry clash revert: symmetry clash REVERT: H 7 MET cc_start: 0.7528 (tmm) cc_final: 0.6884 (tmm) REVERT: H 9 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7900 (ttp80) REVERT: B 494 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7775 (tm-30) REVERT: E 58 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: E 88 ARG cc_start: 0.6949 (ttp-170) cc_final: 0.6691 (ttp80) REVERT: E 254 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7674 (t) REVERT: E 359 ARG cc_start: 0.7846 (ptp90) cc_final: 0.7527 (mtm-85) REVERT: G 34 LEU cc_start: 0.8814 (tp) cc_final: 0.8514 (tt) REVERT: G 49 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7641 (ttp80) REVERT: G 82 ARG cc_start: 0.6702 (tpp-160) cc_final: 0.6361 (tpp-160) REVERT: G 168 TRP cc_start: 0.8306 (m-90) cc_final: 0.7984 (m-90) REVERT: G 249 GLU cc_start: 0.8016 (pp20) cc_final: 0.7527 (pp20) REVERT: C 626 ILE cc_start: 0.8876 (tp) cc_final: 0.8383 (tt) REVERT: F 39 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8365 (tt) REVERT: F 469 ARG cc_start: 0.6941 (tpp80) cc_final: 0.6701 (tpp80) REVERT: I 16 ASP cc_start: 0.7045 (p0) cc_final: 0.6657 (p0) REVERT: I 160 MET cc_start: 0.7997 (ttm) cc_final: 0.7785 (ttm) REVERT: I 205 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: I 265 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: I 309 ASN cc_start: 0.8192 (t0) cc_final: 0.7783 (t0) REVERT: I 601 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7454 (mm) REVERT: I 733 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8480 (tp) REVERT: D 94 MET cc_start: 0.4019 (ttt) cc_final: 0.3174 (tpt) REVERT: D 274 ILE cc_start: 0.3839 (OUTLIER) cc_final: 0.3410 (mt) REVERT: D 307 ASN cc_start: 0.7720 (t0) cc_final: 0.7460 (t0) REVERT: D 347 MET cc_start: 0.6150 (mmm) cc_final: 0.5927 (mmm) REVERT: D 567 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8612 (mt) REVERT: D 581 HIS cc_start: 0.6672 (OUTLIER) cc_final: 0.6085 (m90) REVERT: D 583 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7862 (t0) REVERT: D 590 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.5036 (pp) outliers start: 100 outliers final: 58 residues processed: 452 average time/residue: 0.3654 time to fit residues: 268.1447 Evaluate side-chains 425 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 355 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 205 TYR Chi-restraints excluded: chain I residue 265 GLU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 375 GLU Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 601 ILE Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 744 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 590 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 123 optimal weight: 1.9990 chunk 329 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 366 optimal weight: 1.9990 chunk 304 optimal weight: 9.9990 chunk 169 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 192 optimal weight: 50.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 608 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 ASN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 GLN F 265 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN I 316 GLN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 652 HIS ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 27917 Z= 0.423 Angle : 0.711 14.503 37936 Z= 0.361 Chirality : 0.048 0.209 4464 Planarity : 0.004 0.048 4968 Dihedral : 5.197 53.368 4041 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.44 % Favored : 91.51 % Rotamer: Outliers : 5.46 % Allowed : 23.01 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3767 helix: 1.17 (0.14), residues: 1320 sheet: -1.43 (0.18), residues: 843 loop : -2.49 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 237 HIS 0.026 0.002 HIS E 249 PHE 0.034 0.002 PHE I 45 TYR 0.025 0.002 TYR E 218 ARG 0.004 0.001 ARG D 368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 359 time to evaluate : 3.287 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: symmetry clash revert: symmetry clash REVERT: H 7 MET cc_start: 0.7393 (tmm) cc_final: 0.6654 (tmm) REVERT: H 9 ARG cc_start: 0.8324 (ttp-110) cc_final: 0.8042 (ttp80) REVERT: E 88 ARG cc_start: 0.7167 (ttp-170) cc_final: 0.6946 (ttp80) REVERT: E 235 ASN cc_start: 0.7541 (t0) cc_final: 0.7324 (t0) REVERT: G 34 LEU cc_start: 0.8840 (tp) cc_final: 0.8587 (tt) REVERT: G 49 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7537 (ttp80) REVERT: G 82 ARG cc_start: 0.6780 (tpp-160) cc_final: 0.6434 (tpp-160) REVERT: G 249 GLU cc_start: 0.8027 (pp20) cc_final: 0.7425 (pp20) REVERT: C 681 LYS cc_start: 0.6121 (OUTLIER) cc_final: 0.4930 (mttt) REVERT: F 39 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8548 (tt) REVERT: F 54 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7269 (p0) REVERT: F 62 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7730 (mm-30) REVERT: F 265 ASN cc_start: 0.8060 (m-40) cc_final: 0.7518 (m110) REVERT: I 16 ASP cc_start: 0.7272 (p0) cc_final: 0.6768 (p0) REVERT: I 160 MET cc_start: 0.8021 (ttm) cc_final: 0.7818 (ttm) REVERT: I 205 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: I 265 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: I 271 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7842 (mt) REVERT: I 290 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8883 (p90) REVERT: I 309 ASN cc_start: 0.8176 (t0) cc_final: 0.7758 (t0) REVERT: I 462 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7334 (mm-40) REVERT: I 733 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8456 (tp) REVERT: D 94 MET cc_start: 0.3603 (ttt) cc_final: 0.2598 (tpt) REVERT: D 274 ILE cc_start: 0.3671 (OUTLIER) cc_final: 0.3242 (mt) REVERT: D 307 ASN cc_start: 0.7722 (t0) cc_final: 0.7478 (t0) REVERT: D 567 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8651 (mt) REVERT: D 581 HIS cc_start: 0.6608 (OUTLIER) cc_final: 0.5980 (m90) REVERT: D 583 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7988 (t0) outliers start: 136 outliers final: 91 residues processed: 457 average time/residue: 0.3673 time to fit residues: 274.3308 Evaluate side-chains 452 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 349 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 477 SER Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain I residue 205 TYR Chi-restraints excluded: chain I residue 265 GLU Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 284 ASP Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 459 ILE Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 522 VAL Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 601 ILE Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 744 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 590 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 353 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 208 optimal weight: 0.6980 chunk 267 optimal weight: 3.9990 chunk 207 optimal weight: 0.0570 chunk 308 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 365 optimal weight: 1.9990 chunk 228 optimal weight: 0.5980 chunk 222 optimal weight: 0.4980 chunk 168 optimal weight: 40.0000 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN G 174 GLN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27917 Z= 0.193 Angle : 0.607 13.850 37936 Z= 0.309 Chirality : 0.044 0.200 4464 Planarity : 0.004 0.049 4968 Dihedral : 4.843 52.715 4041 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 3.98 % Allowed : 25.10 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.14), residues: 3767 helix: 1.70 (0.14), residues: 1312 sheet: -1.32 (0.18), residues: 851 loop : -2.27 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 212 HIS 0.022 0.001 HIS E 249 PHE 0.027 0.002 PHE D 534 TYR 0.020 0.001 TYR E 218 ARG 0.004 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 368 time to evaluate : 3.285 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 MET cc_start: 0.7360 (tmm) cc_final: 0.6639 (tmm) REVERT: H 9 ARG cc_start: 0.8292 (ttp-110) cc_final: 0.8009 (ttp80) REVERT: B 494 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7686 (tm-30) REVERT: E 232 ASP cc_start: 0.6917 (t0) cc_final: 0.6576 (t0) REVERT: E 246 MET cc_start: 0.7163 (mtt) cc_final: 0.6595 (mtt) REVERT: G 29 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7695 (m) REVERT: G 34 LEU cc_start: 0.8835 (tp) cc_final: 0.8615 (tt) REVERT: G 82 ARG cc_start: 0.6581 (tpp-160) cc_final: 0.6243 (tpp-160) REVERT: G 155 LEU cc_start: 0.8266 (mt) cc_final: 0.8024 (mp) REVERT: G 249 GLU cc_start: 0.8044 (pp20) cc_final: 0.7611 (pp20) REVERT: C 626 ILE cc_start: 0.8812 (tp) cc_final: 0.8298 (tt) REVERT: C 669 ARG cc_start: 0.6356 (mmp80) cc_final: 0.6073 (mmp80) REVERT: F 39 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8378 (tt) REVERT: F 62 GLU cc_start: 0.8006 (mm-30) cc_final: 0.6779 (mm-30) REVERT: F 326 ASP cc_start: 0.8066 (p0) cc_final: 0.7286 (t0) REVERT: I 16 ASP cc_start: 0.7158 (p0) cc_final: 0.6748 (p0) REVERT: I 265 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: I 309 ASN cc_start: 0.8122 (t0) cc_final: 0.7725 (t0) REVERT: D 94 MET cc_start: 0.3564 (ttt) cc_final: 0.2560 (tpt) REVERT: D 274 ILE cc_start: 0.3845 (OUTLIER) cc_final: 0.3427 (mt) REVERT: D 307 ASN cc_start: 0.7695 (t0) cc_final: 0.7475 (t0) REVERT: D 567 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8614 (mt) REVERT: D 581 HIS cc_start: 0.6488 (OUTLIER) cc_final: 0.5918 (m90) REVERT: D 583 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7696 (t0) outliers start: 99 outliers final: 60 residues processed: 437 average time/residue: 0.3680 time to fit residues: 260.2907 Evaluate side-chains 414 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 347 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 265 GLU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 607 GLU Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 225 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 218 optimal weight: 0.0010 chunk 110 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 180 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 chunk 287 optimal weight: 0.6980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN I 316 GLN I 420 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27917 Z= 0.191 Angle : 0.618 14.791 37936 Z= 0.311 Chirality : 0.044 0.239 4464 Planarity : 0.003 0.048 4968 Dihedral : 4.666 50.680 4039 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.34 % Rotamer: Outliers : 3.69 % Allowed : 25.30 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3767 helix: 1.85 (0.14), residues: 1312 sheet: -1.14 (0.18), residues: 851 loop : -2.24 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 9 HIS 0.019 0.001 HIS E 249 PHE 0.027 0.002 PHE D 174 TYR 0.023 0.001 TYR E 218 ARG 0.003 0.000 ARG I 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 367 time to evaluate : 3.012 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: symmetry clash revert: symmetry clash REVERT: H 7 MET cc_start: 0.7261 (tmm) cc_final: 0.6565 (tmm) REVERT: H 9 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.8013 (ttp80) REVERT: H 46 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7649 (ttpp) REVERT: E 232 ASP cc_start: 0.7000 (t0) cc_final: 0.6677 (t0) REVERT: G 29 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7742 (m) REVERT: G 34 LEU cc_start: 0.8826 (tp) cc_final: 0.8615 (tt) REVERT: G 49 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7430 (ttp80) REVERT: G 82 ARG cc_start: 0.6558 (tpp-160) cc_final: 0.6225 (tpp-160) REVERT: G 155 LEU cc_start: 0.8248 (mt) cc_final: 0.7991 (mp) REVERT: G 249 GLU cc_start: 0.8055 (pp20) cc_final: 0.7600 (pp20) REVERT: C 626 ILE cc_start: 0.8777 (tp) cc_final: 0.8271 (tt) REVERT: F 39 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8310 (tt) REVERT: F 62 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7594 (mp0) REVERT: F 326 ASP cc_start: 0.7978 (p0) cc_final: 0.7255 (t0) REVERT: I 265 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: I 309 ASN cc_start: 0.7997 (t0) cc_final: 0.7672 (t0) REVERT: I 459 ILE cc_start: 0.8647 (mp) cc_final: 0.8392 (mp) REVERT: I 601 ILE cc_start: 0.7682 (mm) cc_final: 0.7425 (mm) REVERT: D 94 MET cc_start: 0.3307 (ttt) cc_final: 0.2372 (tpt) REVERT: D 274 ILE cc_start: 0.3881 (OUTLIER) cc_final: 0.3481 (mt) REVERT: D 307 ASN cc_start: 0.7679 (t0) cc_final: 0.7473 (t0) REVERT: D 567 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8587 (mt) REVERT: D 581 HIS cc_start: 0.6316 (OUTLIER) cc_final: 0.5829 (m90) REVERT: D 583 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7817 (t0) outliers start: 92 outliers final: 67 residues processed: 438 average time/residue: 0.3702 time to fit residues: 262.3549 Evaluate side-chains 429 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 355 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 205 TYR Chi-restraints excluded: chain I residue 265 GLU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 607 GLU Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 332 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 319 optimal weight: 0.9980 chunk 340 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 148 optimal weight: 30.0000 chunk 267 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 321 optimal weight: 1.9990 chunk 339 optimal weight: 0.0370 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN I 316 GLN I 420 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27917 Z= 0.337 Angle : 0.675 12.654 37936 Z= 0.343 Chirality : 0.046 0.217 4464 Planarity : 0.004 0.048 4968 Dihedral : 4.913 51.271 4039 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.72 % Favored : 92.25 % Rotamer: Outliers : 3.94 % Allowed : 25.42 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3767 helix: 1.53 (0.14), residues: 1320 sheet: -1.15 (0.18), residues: 836 loop : -2.24 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 237 HIS 0.021 0.002 HIS E 249 PHE 0.042 0.002 PHE I 279 TYR 0.024 0.002 TYR E 218 ARG 0.008 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 352 time to evaluate : 3.056 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: H 7 MET cc_start: 0.7517 (tmm) cc_final: 0.6744 (tmm) REVERT: H 9 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.8041 (ttp-110) REVERT: B 700 ASP cc_start: 0.7245 (m-30) cc_final: 0.6965 (m-30) REVERT: E 361 TYR cc_start: 0.7551 (m-80) cc_final: 0.7055 (m-80) REVERT: G 49 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7444 (ttm-80) REVERT: G 77 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7318 (mt) REVERT: G 82 ARG cc_start: 0.6658 (tpp-160) cc_final: 0.6296 (tpp-160) REVERT: G 249 GLU cc_start: 0.8062 (pp20) cc_final: 0.7398 (pp20) REVERT: C 626 ILE cc_start: 0.8826 (tp) cc_final: 0.8313 (tt) REVERT: F 39 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8493 (tt) REVERT: F 62 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7615 (mp0) REVERT: F 325 THR cc_start: 0.8801 (p) cc_final: 0.8478 (t) REVERT: F 326 ASP cc_start: 0.8198 (p0) cc_final: 0.7516 (t0) REVERT: F 492 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7601 (ttmm) REVERT: I 126 MET cc_start: 0.7243 (mmm) cc_final: 0.7042 (mmm) REVERT: I 205 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: I 265 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: I 309 ASN cc_start: 0.8163 (t0) cc_final: 0.7769 (t0) REVERT: I 459 ILE cc_start: 0.8741 (mp) cc_final: 0.8466 (mp) REVERT: D 94 MET cc_start: 0.3059 (ttt) cc_final: 0.2229 (tpt) REVERT: D 274 ILE cc_start: 0.4014 (OUTLIER) cc_final: 0.3607 (mt) REVERT: D 567 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8626 (mt) REVERT: D 581 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.5971 (m90) REVERT: D 583 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7999 (t0) outliers start: 98 outliers final: 76 residues processed: 425 average time/residue: 0.3699 time to fit residues: 253.6382 Evaluate side-chains 426 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 342 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 205 TYR Chi-restraints excluded: chain I residue 265 GLU Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 607 GLU Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 223 optimal weight: 0.5980 chunk 359 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 170 optimal weight: 50.0000 chunk 250 optimal weight: 0.9980 chunk 377 optimal weight: 0.9980 chunk 347 optimal weight: 20.0000 chunk 300 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 232 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 GLN I 276 GLN I 316 GLN I 420 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27917 Z= 0.235 Angle : 0.637 12.354 37936 Z= 0.322 Chirality : 0.045 0.212 4464 Planarity : 0.004 0.049 4968 Dihedral : 4.769 50.553 4039 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.50 % Rotamer: Outliers : 3.65 % Allowed : 25.78 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.14), residues: 3767 helix: 1.68 (0.14), residues: 1328 sheet: -1.05 (0.19), residues: 826 loop : -2.22 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 9 HIS 0.022 0.001 HIS E 249 PHE 0.027 0.002 PHE D 534 TYR 0.022 0.001 TYR E 218 ARG 0.003 0.000 ARG D 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 358 time to evaluate : 3.140 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: symmetry clash REVERT: H 7 MET cc_start: 0.7288 (tmm) cc_final: 0.6608 (tmm) REVERT: H 9 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7879 (ttp-110) REVERT: H 46 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7719 (ttpp) REVERT: E 88 ARG cc_start: 0.7276 (ttp-170) cc_final: 0.7048 (ttp80) REVERT: E 232 ASP cc_start: 0.7232 (t0) cc_final: 0.6817 (t0) REVERT: E 361 TYR cc_start: 0.7436 (m-80) cc_final: 0.6875 (m-80) REVERT: E 412 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6893 (tm-30) REVERT: E 416 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7526 (mm-30) REVERT: G 49 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7395 (ttm-80) REVERT: G 77 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7275 (mt) REVERT: G 82 ARG cc_start: 0.6629 (tpp-160) cc_final: 0.6286 (tpp-160) REVERT: G 155 LEU cc_start: 0.8231 (mt) cc_final: 0.7993 (mp) REVERT: G 249 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: C 626 ILE cc_start: 0.8794 (tp) cc_final: 0.8279 (tt) REVERT: F 39 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8400 (tt) REVERT: F 62 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7370 (mt-10) REVERT: F 326 ASP cc_start: 0.8088 (p0) cc_final: 0.7353 (t0) REVERT: I 309 ASN cc_start: 0.8129 (t0) cc_final: 0.7748 (t0) REVERT: I 459 ILE cc_start: 0.8658 (mp) cc_final: 0.8414 (mp) REVERT: D 94 MET cc_start: 0.3222 (ttt) cc_final: 0.2317 (tpt) REVERT: D 274 ILE cc_start: 0.3931 (OUTLIER) cc_final: 0.3538 (mt) REVERT: D 567 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8614 (mt) REVERT: D 581 HIS cc_start: 0.6437 (OUTLIER) cc_final: 0.5911 (m90) REVERT: D 583 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.8042 (t0) outliers start: 91 outliers final: 76 residues processed: 426 average time/residue: 0.3590 time to fit residues: 247.4544 Evaluate side-chains 432 residues out of total 3342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 349 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 607 GLU Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 654 GLU Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 723 SER Chi-restraints excluded: chain I residue 733 LEU Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 238 optimal weight: 0.8980 chunk 320 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 301 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 38 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN I 316 GLN I 420 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.201768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.152322 restraints weight = 34147.991| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.83 r_work: 0.3376 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27917 Z= 0.292 Angle : 0.649 12.487 37936 Z= 0.330 Chirality : 0.046 0.210 4464 Planarity : 0.004 0.049 4968 Dihedral : 4.801 53.139 4039 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.41 % Favored : 92.57 % Rotamer: Outliers : 3.69 % Allowed : 26.02 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.14), residues: 3767 helix: 1.59 (0.14), residues: 1328 sheet: -1.05 (0.18), residues: 841 loop : -2.21 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 9 HIS 0.022 0.001 HIS E 249 PHE 0.028 0.002 PHE D 534 TYR 0.023 0.001 TYR E 218 ARG 0.004 0.000 ARG D 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6158.18 seconds wall clock time: 112 minutes 29.55 seconds (6749.55 seconds total)