Starting phenix.real_space_refine on Tue Feb 20 04:22:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voa_21259/02_2024/6voa_21259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voa_21259/02_2024/6voa_21259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voa_21259/02_2024/6voa_21259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voa_21259/02_2024/6voa_21259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voa_21259/02_2024/6voa_21259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voa_21259/02_2024/6voa_21259.pdb" } resolution = 4.0 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= 0.002 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 95 5.16 5 C 16810 2.51 5 N 4832 2.21 5 O 5087 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 632": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B TYR 644": "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 49": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" 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 58": "OE1" <-> "OE2" 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26824 Number of models: 1 Model: "" Number of chains: 9 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: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 3465 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 414} Link IDs: {'PTRANS': 17, 'TRANS': 601} Chain breaks: 6 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1447 Unresolved non-hydrogen angles: 1874 Unresolved non-hydrogen dihedrals: 1184 Unresolved non-hydrogen chiralities: 150 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 15, 'TYR:plan': 15, 'ASN:plan1': 25, 'TRP:plan': 4, 'ASP:plan': 32, 'PHE:plan': 23, 'GLU:plan': 27, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 802 Chain: "E" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3114 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 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: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 3676 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 484} Link IDs: {'PTRANS': 25, 'TRANS': 641} Chain breaks: 8 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1687 Unresolved non-hydrogen angles: 2159 Unresolved non-hydrogen dihedrals: 1384 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': 37, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 910 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: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 816 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 5, 'TRANS': 159} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 676 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 13, 'PHE:plan': 7, 'GLU:plan': 8, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 275 Chain: "D" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3090 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 33, 'TRANS': 494} Chain breaks: 2 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1373 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 16, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 12, 'GLU:plan': 23, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 515 Time building chain proxies: 14.49, per 1000 atoms: 0.54 Number of scatterers: 26824 At special positions: 0 Unit cell: (125.28, 150.12, 207.36, 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 95 16.00 O 5087 8.00 N 4832 7.00 C 16810 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: 9.55 Conformation dependent library (CDL) restraints added in 5.6 seconds 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7454 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 45 sheets defined 35.3% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 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 506 through 517 Processing helix chain 'B' and resid 560 through 575 removed outlier: 3.730A pdb=" N ALA B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 634 removed outlier: 3.687A pdb=" N GLU B 592 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 4.027A 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 688 through 703 removed outlier: 3.847A pdb=" N ASN B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 694 " --> pdb=" O PRO B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'E' and resid 35 through 45 removed outlier: 3.738A pdb=" N ILE E 39 " --> pdb=" O GLN E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 63 Processing helix chain 'E' and resid 68 through 80 removed outlier: 3.551A pdb=" N VAL E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.678A 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: 3.751A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 148 removed outlier: 4.272A 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: 3.980A 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: 3.806A 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: 3.903A 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 350 removed outlier: 3.755A pdb=" N ASN E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) 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: 3.759A 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: 3.868A 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: 4.937A pdb=" N ALA C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.917A pdb=" N ASN C 638 " --> pdb=" O HIS C 635 " (cutoff:3.500A) removed outlier: 3.754A 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: 3.825A pdb=" N GLU C 651 " --> pdb=" O ARG C 647 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 652 " --> pdb=" O CYS C 648 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASP C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 5.757A 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: 3.616A 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: 3.617A pdb=" N GLN F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 48 removed outlier: 3.608A pdb=" N TRP F 37 " --> pdb=" O ASP F 33 " (cutoff:3.500A) removed outlier: 3.881A 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 60 through 66 removed outlier: 3.505A pdb=" N ILE F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.644A 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: 3.650A 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: 3.689A 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: 3.746A 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: 4.168A pdb=" N TRP I 610 " --> pdb=" O PHE I 606 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU I 611 " --> pdb=" O GLU I 607 " (cutoff:3.500A) removed outlier: 4.093A 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 'A' and resid 32 through 37 removed outlier: 4.452A pdb=" N LYS A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.507A pdb=" N LYS A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.817A pdb=" N LEU D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 141 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.542A 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 6 through 9 removed outlier: 4.768A pdb=" N GLU B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.889A 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: 6.549A pdb=" N ASP B 104 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.181A 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: 4.393A 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: 4.422A 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: 6.777A 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: 4.671A 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: 4.422A 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: 6.777A 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 553 through 556 Processing sheet with id=AB4, first strand: chain 'G' and resid 13 through 15 removed outlier: 3.521A 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: 4.205A 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: 4.127A 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: 4.102A 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: 6.803A 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: 6.885A 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: 3.954A 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: 3.798A 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: 6.264A pdb=" N CYS C 133 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 5.868A 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: 4.053A pdb=" N ASP C 282 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.629A 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: 5.560A pdb=" N TYR I 358 " --> pdb=" O ASP I 8 " (cutoff:3.500A) removed outlier: 4.314A 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: 3.580A 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: 4.640A pdb=" N MET I 311 " --> pdb=" O ASN I 307 " (cutoff:3.500A) removed outlier: 6.554A 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: 3.733A 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: 5.574A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.311A 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 'A' and resid 21 through 22 removed outlier: 3.878A pdb=" N CYS A 22 " --> pdb=" O PHE A 68 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AE5, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AE6, first strand: chain 'D' and resid 265 through 266 Processing sheet with id=AE7, first strand: chain 'D' and resid 296 through 297 Processing sheet with id=AE8, first strand: chain 'D' and resid 487 through 493 Processing sheet with id=AE9, first strand: chain 'D' and resid 534 through 536 1393 hydrogen bonds defined for protein. 4014 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: 9.85 Time building geometry restraints manager: 10.41 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: 4782 1.32 - 1.44: 6541 1.44 - 1.57: 15715 1.57 - 1.69: 0 1.69 - 1.82: 144 Bond restraints: 27182 Sorted by residual: bond pdb=" CA SER C 430 " pdb=" CB SER C 430 " ideal model delta sigma weight residual 1.530 1.457 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CA ALA B 167 " pdb=" CB ALA B 167 " ideal model delta sigma weight residual 1.534 1.473 0.061 1.76e-02 3.23e+03 1.18e+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 1.07e+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 1.195 0.037 1.16e-02 7.43e+03 1.04e+01 ... (remaining 27177 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.40: 593 106.40 - 113.33: 14874 113.33 - 120.27: 9664 120.27 - 127.21: 11715 127.21 - 134.14: 188 Bond angle restraints: 37034 Sorted by residual: angle pdb=" C GLY C 327 " pdb=" N PRO C 328 " pdb=" CA PRO C 328 " ideal model delta sigma weight residual 119.84 133.68 -13.84 1.25e+00 6.40e-01 1.23e+02 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 7.04e+01 angle pdb=" C MET D 326 " pdb=" N PRO D 327 " pdb=" CA PRO D 327 " ideal model delta sigma weight residual 119.05 127.59 -8.54 1.11e+00 8.12e-01 5.92e+01 angle pdb=" N GLU D 164 " pdb=" CA GLU D 164 " pdb=" C GLU D 164 " ideal model delta sigma weight residual 111.28 119.29 -8.01 1.09e+00 8.42e-01 5.40e+01 angle pdb=" N CYS A 160 " pdb=" CA CYS A 160 " pdb=" C CYS A 160 " ideal model delta sigma weight residual 108.45 117.65 -9.20 1.26e+00 6.30e-01 5.33e+01 ... (remaining 37029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14888 18.00 - 35.99: 1128 35.99 - 53.99: 189 53.99 - 71.99: 40 71.99 - 89.98: 20 Dihedral angle restraints: 16265 sinusoidal: 4791 harmonic: 11474 Sorted by residual: dihedral pdb=" CA LEU D 179 " pdb=" C LEU D 179 " pdb=" N SER D 180 " pdb=" CA SER D 180 " ideal model delta harmonic sigma weight residual 180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 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 -137.25 14.65 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" CA LYS D 69 " pdb=" C LYS D 69 " pdb=" N VAL D 70 " pdb=" CA VAL D 70 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 16262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4093 0.098 - 0.196: 298 0.196 - 0.294: 36 0.294 - 0.391: 10 0.391 - 0.489: 3 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CA ILE A 90 " pdb=" N ILE A 90 " pdb=" C ILE A 90 " pdb=" CB ILE A 90 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 5.99e+00 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 5.72e+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 5.50e+00 ... (remaining 4437 not shown) Planarity restraints: 4915 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 3.22e-02 1.04e+01 pdb=" C PHE B 250 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE B 250 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 251 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 322 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.16e+00 pdb=" C TRP D 322 " -0.049 2.00e-02 2.50e+03 pdb=" O TRP D 322 " 0.019 2.00e-02 2.50e+03 pdb=" N THR D 323 " 0.016 2.00e-02 2.50e+03 ... (remaining 4912 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 13 1.87 - 2.62: 324 2.62 - 3.38: 35004 3.38 - 4.14: 59291 4.14 - 4.90: 109571 Nonbonded interactions: 204203 Sorted by model distance: nonbonded pdb=" CB SER C 428 " pdb=" C THR C 444 " model vdw 1.107 3.670 nonbonded pdb=" CB SER C 428 " pdb=" O THR C 444 " model vdw 1.299 3.440 nonbonded pdb=" CB SER C 428 " pdb=" CA THR C 444 " model vdw 1.335 3.870 nonbonded pdb=" CA SER C 428 " pdb=" O THR C 444 " model vdw 1.484 3.470 nonbonded pdb=" CA GLY A 52 " pdb=" O ASP A 69 " model vdw 1.504 3.440 ... (remaining 204198 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 10.850 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 70.180 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 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 0.073 27182 Z= 0.286 Angle : 0.834 13.837 37034 Z= 0.541 Chirality : 0.057 0.489 4440 Planarity : 0.004 0.050 4915 Dihedral : 14.092 89.984 8811 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.77 % Favored : 90.72 % Rotamer: Outliers : 1.57 % Allowed : 5.91 % Favored : 92.52 % Cbeta Deviations : 0.21 % 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: -3.28 (0.12), residues: 3888 helix: -0.64 (0.13), residues: 1331 sheet: -2.26 (0.17), residues: 804 loop : -3.41 (0.12), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 237 HIS 0.006 0.001 HIS G 190 PHE 0.016 0.002 PHE C 678 TYR 0.016 0.001 TYR E 124 ARG 0.008 0.000 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 668 time to evaluate : 3.106 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 591 GLU cc_start: 0.7190 (pp20) cc_final: 0.6918 (tm-30) REVERT: B 599 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7371 (mmmt) REVERT: B 705 ASN cc_start: 0.6740 (m-40) cc_final: 0.5625 (t0) REVERT: E 306 ILE cc_start: 0.7003 (mt) cc_final: 0.6219 (tp) REVERT: G 22 MET cc_start: 0.6610 (mtm) cc_final: 0.6369 (ptm) REVERT: G 131 TYR cc_start: 0.7115 (t80) cc_final: 0.6740 (t80) REVERT: G 190 HIS cc_start: 0.4866 (p-80) cc_final: 0.4154 (p-80) REVERT: F 202 SER cc_start: 0.8439 (m) cc_final: 0.7673 (t) REVERT: I 160 MET cc_start: 0.6450 (ttt) cc_final: 0.6096 (tpt) REVERT: I 699 LEU cc_start: 0.7218 (tp) cc_final: 0.7008 (tp) REVERT: D 586 MET cc_start: 0.6061 (mpp) cc_final: 0.5364 (mmm) outliers start: 33 outliers final: 8 residues processed: 696 average time/residue: 0.3945 time to fit residues: 424.5597 Evaluate side-chains 305 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 297 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain I residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 20.0000 chunk 296 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 158 optimal weight: 40.0000 chunk 306 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 186 optimal weight: 50.0000 chunk 228 optimal weight: 6.9990 chunk 355 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 693 GLN B 705 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 140 ASN E 157 GLN ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 HIS E 319 GLN E 375 ASN E 377 ASN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN G 102 ASN G 128 HIS ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 188 HIS ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN F 241 GLN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 309 ASN F 311 HIS F 351 ASN ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 435 GLN ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 496 GLN I 37 GLN I 117 HIS ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 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** ** I 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 693 GLN I 694 HIS I 705 GLN ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 GLN I 764 GLN ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.109 27182 Z= 0.644 Angle : 1.115 17.604 37034 Z= 0.584 Chirality : 0.057 0.311 4440 Planarity : 0.008 0.102 4915 Dihedral : 7.139 75.378 4142 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 27.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.96 % Favored : 88.86 % Rotamer: Outliers : 8.01 % Allowed : 18.35 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.97 (0.12), residues: 3888 helix: -0.52 (0.13), residues: 1364 sheet: -1.71 (0.18), residues: 753 loop : -3.33 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 273 HIS 0.025 0.004 HIS D 504 PHE 0.064 0.005 PHE F 16 TYR 0.035 0.004 TYR I 645 ARG 0.012 0.002 ARG F 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 260 time to evaluate : 2.983 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: B 599 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8141 (mmmt) REVERT: B 673 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6466 (tppt) REVERT: E 306 ILE cc_start: 0.8190 (mt) cc_final: 0.7967 (mt) REVERT: E 315 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7561 (tp) REVERT: E 331 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7636 (mt) REVERT: G 39 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7934 (t0) REVERT: G 96 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: G 120 LEU cc_start: 0.8016 (tp) cc_final: 0.7671 (tt) REVERT: G 181 PHE cc_start: 0.5521 (m-80) cc_final: 0.4933 (m-80) REVERT: G 190 HIS cc_start: 0.5368 (p-80) cc_final: 0.4909 (p-80) REVERT: F 56 ASP cc_start: 0.8269 (t70) cc_final: 0.7954 (t0) REVERT: F 58 GLU cc_start: 0.5856 (OUTLIER) cc_final: 0.4689 (mp0) REVERT: F 122 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: F 243 MET cc_start: 0.7108 (mmm) cc_final: 0.6825 (mmm) REVERT: F 252 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8132 (mtmm) REVERT: F 266 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7441 (tp) REVERT: F 384 ASP cc_start: 0.6475 (m-30) cc_final: 0.6046 (m-30) REVERT: I 16 ASP cc_start: 0.5620 (t0) cc_final: 0.4522 (t0) REVERT: I 280 MET cc_start: 0.6108 (ptm) cc_final: 0.5643 (ptm) REVERT: I 308 HIS cc_start: 0.5957 (OUTLIER) cc_final: 0.5501 (m90) REVERT: D 586 MET cc_start: 0.6453 (mpp) cc_final: 0.5248 (mtp) outliers start: 168 outliers final: 93 residues processed: 387 average time/residue: 0.3259 time to fit residues: 209.2879 Evaluate side-chains 303 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 200 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 700 ASP Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 395 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 96 TYR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 302 TYR Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 267 PHE Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 294 CYS Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 308 HIS Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 462 GLN Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 676 ILE Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 694 HIS Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 510 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 524 ASN Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 587 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 295 optimal weight: 6.9990 chunk 241 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 355 optimal weight: 20.0000 chunk 384 optimal weight: 4.9990 chunk 316 optimal weight: 0.9990 chunk 352 optimal weight: 50.0000 chunk 121 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 ASN ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS F 216 GLN F 388 ASN F 413 ASN ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 488 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 471 GLN I 515 ASN I 652 HIS I 677 GLN I 694 HIS ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27182 Z= 0.228 Angle : 0.660 10.278 37034 Z= 0.346 Chirality : 0.045 0.183 4440 Planarity : 0.004 0.058 4915 Dihedral : 5.609 81.293 4134 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.92 % Favored : 92.03 % Rotamer: Outliers : 5.72 % Allowed : 22.40 % Favored : 71.88 % 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: -2.07 (0.13), residues: 3888 helix: 0.51 (0.13), residues: 1371 sheet: -1.45 (0.18), residues: 765 loop : -2.98 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 610 HIS 0.008 0.001 HIS D 449 PHE 0.044 0.002 PHE E 413 TYR 0.035 0.002 TYR B 589 ARG 0.015 0.001 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 241 time to evaluate : 4.582 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: E 44 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7420 (tt) REVERT: E 306 ILE cc_start: 0.7688 (mt) cc_final: 0.7467 (mt) REVERT: E 417 MET cc_start: 0.7017 (ttp) cc_final: 0.6776 (ttm) REVERT: G 95 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7190 (tt) REVERT: G 181 PHE cc_start: 0.5049 (m-80) cc_final: 0.4528 (m-80) REVERT: G 190 HIS cc_start: 0.4866 (p-80) cc_final: 0.4552 (p-80) REVERT: G 237 ILE cc_start: 0.5764 (OUTLIER) cc_final: 0.5509 (tp) REVERT: F 137 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7256 (pt) REVERT: F 238 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8277 (tt) REVERT: F 243 MET cc_start: 0.6760 (mmm) cc_final: 0.6486 (mmm) REVERT: I 280 MET cc_start: 0.5753 (ptm) cc_final: 0.5261 (ptm) REVERT: I 324 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8739 (m) REVERT: I 462 GLN cc_start: 0.2897 (mm-40) cc_final: 0.2280 (mm-40) REVERT: D 586 MET cc_start: 0.6023 (mpp) cc_final: 0.5526 (mmm) outliers start: 120 outliers final: 63 residues processed: 330 average time/residue: 0.3599 time to fit residues: 198.6502 Evaluate side-chains 272 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 203 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 63 HIS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 319 GLN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 550 ILE Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 603 SER Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 351 optimal weight: 40.0000 chunk 267 optimal weight: 10.0000 chunk 184 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 169 optimal weight: 30.0000 chunk 238 optimal weight: 4.9990 chunk 356 optimal weight: 20.0000 chunk 377 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 chunk 338 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 HIS ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 ASN ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS F 216 GLN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 587 GLN I 794 ASN ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 581 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.110 27182 Z= 0.777 Angle : 1.177 17.609 37034 Z= 0.616 Chirality : 0.059 0.389 4440 Planarity : 0.008 0.110 4915 Dihedral : 7.450 51.669 4130 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 33.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.63 % Favored : 86.06 % Rotamer: Outliers : 9.91 % Allowed : 22.12 % Favored : 67.97 % 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: -3.35 (0.12), residues: 3888 helix: -1.13 (0.12), residues: 1351 sheet: -1.85 (0.18), residues: 744 loop : -3.31 (0.13), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP I 741 HIS 0.017 0.004 HIS I 73 PHE 0.052 0.005 PHE E 90 TYR 0.043 0.004 TYR B 589 ARG 0.045 0.002 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 187 time to evaluate : 3.203 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: B 599 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7977 (mmmt) REVERT: B 673 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6714 (tppt) REVERT: E 44 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7825 (tt) REVERT: G 40 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7030 (t) REVERT: G 95 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7373 (tt) REVERT: G 181 PHE cc_start: 0.5382 (m-80) cc_final: 0.4758 (m-80) REVERT: F 63 MET cc_start: 0.7818 (mtt) cc_final: 0.7557 (mtm) REVERT: F 137 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7708 (pt) REVERT: F 457 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.6658 (t80) REVERT: I 95 LEU cc_start: 0.5611 (OUTLIER) cc_final: 0.5094 (tt) REVERT: I 462 GLN cc_start: 0.3976 (mm-40) cc_final: 0.3243 (mm-40) REVERT: D 558 LYS cc_start: 0.6796 (mttt) cc_final: 0.6326 (tttt) REVERT: D 586 MET cc_start: 0.6441 (mpp) cc_final: 0.5671 (mtp) outliers start: 208 outliers final: 147 residues processed: 362 average time/residue: 0.3277 time to fit residues: 201.0162 Evaluate side-chains 326 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 172 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 700 ASP Chi-restraints excluded: chain B residue 705 ASN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 282 CYS Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 405 CYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 449 HIS Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 457 PHE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 477 SER Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 ASP Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain I residue 294 CYS Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 603 SER Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 676 ILE Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain I residue 694 HIS Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 737 LEU Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 749 ILE Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 524 ASN Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 587 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 314 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 281 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 339 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN G 157 GLN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 ASN G 251 ASN G 334 GLN ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS F 388 ASN ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN I 120 GLN I 448 ASN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 GLN ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 778 HIS I 794 ASN ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 27182 Z= 0.208 Angle : 0.671 12.464 37034 Z= 0.350 Chirality : 0.045 0.328 4440 Planarity : 0.004 0.060 4915 Dihedral : 5.624 56.017 4130 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.41 % Favored : 92.54 % Rotamer: Outliers : 6.05 % Allowed : 25.45 % Favored : 68.49 % 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: -2.22 (0.13), residues: 3888 helix: 0.33 (0.13), residues: 1359 sheet: -1.73 (0.18), residues: 753 loop : -2.87 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 8 HIS 0.006 0.001 HIS I 732 PHE 0.028 0.002 PHE F 108 TYR 0.022 0.002 TYR C 660 ARG 0.009 0.001 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 220 time to evaluate : 3.372 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: B 679 ILE cc_start: 0.8148 (mm) cc_final: 0.7926 (mm) REVERT: B 714 MET cc_start: 0.8211 (ptp) cc_final: 0.7958 (ptm) REVERT: E 44 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7870 (tt) REVERT: C 622 LYS cc_start: 0.7727 (mptt) cc_final: 0.7446 (ttmt) REVERT: F 137 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7374 (pt) REVERT: F 252 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7935 (mtmm) REVERT: F 380 GLU cc_start: 0.7287 (tp30) cc_final: 0.6707 (tm-30) REVERT: I 95 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.4461 (tt) REVERT: I 416 MET cc_start: 0.7369 (mmm) cc_final: 0.7123 (mmt) REVERT: I 462 GLN cc_start: 0.3298 (mm-40) cc_final: 0.2984 (mm-40) REVERT: I 679 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7085 (tpt170) REVERT: D 558 LYS cc_start: 0.6428 (mttt) cc_final: 0.6164 (tptt) REVERT: D 586 MET cc_start: 0.6015 (mpp) cc_final: 0.5798 (mmm) outliers start: 127 outliers final: 81 residues processed: 314 average time/residue: 0.3223 time to fit residues: 170.0661 Evaluate side-chains 294 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 208 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 157 GLN Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 279 CYS Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 395 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 319 GLU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 517 ASP Chi-restraints excluded: chain I residue 550 ILE Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 603 SER Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 524 ASN Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 378 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 ASN F 416 HIS ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 325 GLN ** I 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 651 HIS ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.7011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 27182 Z= 0.428 Angle : 0.816 12.876 37034 Z= 0.427 Chirality : 0.049 0.285 4440 Planarity : 0.005 0.073 4915 Dihedral : 6.068 57.359 4130 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.75 % Favored : 88.12 % Rotamer: Outliers : 7.58 % Allowed : 25.79 % Favored : 66.63 % 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: -2.43 (0.13), residues: 3888 helix: 0.06 (0.13), residues: 1360 sheet: -1.70 (0.18), residues: 744 loop : -2.98 (0.13), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP I 9 HIS 0.010 0.002 HIS I 73 PHE 0.030 0.003 PHE G 197 TYR 0.020 0.002 TYR C 660 ARG 0.011 0.001 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 200 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 ILE cc_start: 0.8526 (tt) cc_final: 0.8086 (tt) REVERT: E 417 MET cc_start: 0.7720 (ttt) cc_final: 0.7257 (ttp) REVERT: C 622 LYS cc_start: 0.7720 (mptt) cc_final: 0.7476 (ttmt) REVERT: F 26 MET cc_start: 0.7175 (ptt) cc_final: 0.6803 (ptt) REVERT: F 137 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7524 (pt) REVERT: F 243 MET cc_start: 0.7227 (mmm) cc_final: 0.6750 (mmm) REVERT: F 357 PHE cc_start: 0.8046 (t80) cc_final: 0.7264 (t80) REVERT: F 463 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7445 (tptt) REVERT: I 75 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.5593 (mmp80) REVERT: I 95 LEU cc_start: 0.5227 (OUTLIER) cc_final: 0.4793 (tt) REVERT: I 349 SER cc_start: 0.8814 (t) cc_final: 0.8411 (p) REVERT: I 416 MET cc_start: 0.7396 (mmm) cc_final: 0.6898 (mmt) REVERT: I 462 GLN cc_start: 0.3637 (mm-40) cc_final: 0.3145 (mm-40) REVERT: I 692 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7757 (mt) REVERT: D 558 LYS cc_start: 0.6527 (mttt) cc_final: 0.6076 (tttt) REVERT: D 586 MET cc_start: 0.6260 (mpp) cc_final: 0.5943 (mmm) outliers start: 159 outliers final: 115 residues processed: 327 average time/residue: 0.3294 time to fit residues: 180.3738 Evaluate side-chains 314 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 194 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 319 GLU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain I residue 517 ASP Chi-restraints excluded: chain I residue 543 THR Chi-restraints excluded: chain I residue 547 LYS Chi-restraints excluded: chain I residue 550 ILE Chi-restraints excluded: chain I residue 609 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 676 ILE Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 692 LEU Chi-restraints excluded: chain I residue 694 HIS Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 524 ASN Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 215 optimal weight: 0.9990 chunk 276 optimal weight: 0.5980 chunk 214 optimal weight: 3.9990 chunk 318 optimal weight: 8.9990 chunk 211 optimal weight: 0.0980 chunk 376 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 229 optimal weight: 0.5980 chunk 173 optimal weight: 40.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 GLN B 651 ASN ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS E 201 ASN ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN G 194 ASN G 334 GLN C 610 HIS C 633 GLN C 635 HIS ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 27182 Z= 0.190 Angle : 0.633 11.664 37034 Z= 0.329 Chirality : 0.044 0.421 4440 Planarity : 0.004 0.062 4915 Dihedral : 5.180 54.359 4130 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer: Outliers : 5.24 % Allowed : 27.50 % Favored : 67.25 % 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: -1.76 (0.13), residues: 3888 helix: 0.78 (0.14), residues: 1363 sheet: -1.42 (0.19), residues: 744 loop : -2.70 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 610 HIS 0.015 0.001 HIS I 99 PHE 0.022 0.002 PHE F 108 TYR 0.028 0.001 TYR C 660 ARG 0.008 0.001 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 224 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 93 CYS cc_start: 0.7483 (OUTLIER) cc_final: 0.5943 (t) REVERT: E 315 LEU cc_start: 0.7466 (tp) cc_final: 0.7181 (tp) REVERT: E 417 MET cc_start: 0.7491 (ttt) cc_final: 0.6996 (ttp) REVERT: F 26 MET cc_start: 0.7270 (ptt) cc_final: 0.6946 (ptt) REVERT: F 137 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7219 (pt) REVERT: F 243 MET cc_start: 0.7424 (mmm) cc_final: 0.7066 (mmp) REVERT: F 257 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6467 (tt) REVERT: F 357 PHE cc_start: 0.7948 (t80) cc_final: 0.7370 (t80) REVERT: F 380 GLU cc_start: 0.7244 (tp30) cc_final: 0.6733 (tm-30) REVERT: I 75 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.5372 (mmp80) REVERT: I 95 LEU cc_start: 0.4680 (OUTLIER) cc_final: 0.4192 (tt) REVERT: I 588 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.7303 (m) REVERT: I 679 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7174 (tpt170) REVERT: I 692 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7634 (mt) REVERT: D 558 LYS cc_start: 0.6287 (mttt) cc_final: 0.5927 (tttt) outliers start: 110 outliers final: 79 residues processed: 306 average time/residue: 0.3239 time to fit residues: 167.6110 Evaluate side-chains 291 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 204 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 395 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 319 GLU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 254 ILE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 517 ASP Chi-restraints excluded: chain I residue 547 LYS Chi-restraints excluded: chain I residue 550 ILE Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 692 LEU Chi-restraints excluded: chain I residue 740 LEU Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 524 ASN Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 3.9990 chunk 150 optimal weight: 50.0000 chunk 225 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 186 optimal weight: 50.0000 chunk 35 optimal weight: 7.9990 chunk 296 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 325 GLN ** I 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.7435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 27182 Z= 0.445 Angle : 0.828 12.372 37034 Z= 0.434 Chirality : 0.050 0.363 4440 Planarity : 0.005 0.078 4915 Dihedral : 5.975 56.267 4130 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.68 % Favored : 88.17 % Rotamer: Outliers : 7.05 % Allowed : 26.60 % Favored : 66.35 % 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: -2.27 (0.13), residues: 3888 helix: 0.21 (0.13), residues: 1360 sheet: -1.70 (0.18), residues: 754 loop : -2.86 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP I 610 HIS 0.010 0.002 HIS I 73 PHE 0.026 0.003 PHE I 268 TYR 0.030 0.003 TYR C 660 ARG 0.009 0.001 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 195 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 ILE cc_start: 0.8566 (tt) cc_final: 0.8182 (tt) REVERT: E 342 MET cc_start: 0.8405 (ppp) cc_final: 0.7606 (ppp) REVERT: F 26 MET cc_start: 0.7484 (ptt) cc_final: 0.7186 (ptt) REVERT: F 110 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.5225 (ptt-90) REVERT: F 137 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7425 (pt) REVERT: F 357 PHE cc_start: 0.8097 (t80) cc_final: 0.7377 (t80) REVERT: F 463 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7418 (tptt) REVERT: I 75 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.5554 (mmp80) REVERT: I 95 LEU cc_start: 0.5298 (OUTLIER) cc_final: 0.4726 (tt) REVERT: I 679 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7246 (tpt170) REVERT: D 558 LYS cc_start: 0.6448 (mttt) cc_final: 0.6126 (tttt) outliers start: 148 outliers final: 105 residues processed: 308 average time/residue: 0.3327 time to fit residues: 172.0397 Evaluate side-chains 297 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 186 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 319 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 622 LYS Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 220 CYS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 344 TYR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 451 TYR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 486 ASP Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 517 ASP Chi-restraints excluded: chain I residue 547 LYS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 676 ILE Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain I residue 694 HIS Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain I residue 740 LEU Chi-restraints excluded: chain I residue 747 ASP Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain I residue 776 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 524 ASN Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 342 optimal weight: 20.0000 chunk 361 optimal weight: 20.0000 chunk 329 optimal weight: 30.0000 chunk 351 optimal weight: 40.0000 chunk 360 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 275 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 317 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS F 259 GLN F 404 GLN ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 325 GLN ** I 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.7444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 27182 Z= 0.257 Angle : 0.679 12.131 37034 Z= 0.353 Chirality : 0.045 0.295 4440 Planarity : 0.004 0.069 4915 Dihedral : 5.442 55.414 4130 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.80 % Favored : 91.15 % Rotamer: Outliers : 4.96 % Allowed : 28.27 % Favored : 66.78 % 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: -1.94 (0.13), residues: 3888 helix: 0.63 (0.14), residues: 1356 sheet: -1.57 (0.19), residues: 740 loop : -2.77 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 610 HIS 0.024 0.002 HIS I 732 PHE 0.023 0.002 PHE F 160 TYR 0.033 0.002 TYR C 660 ARG 0.008 0.001 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 204 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 630 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6708 (p0) REVERT: B 679 ILE cc_start: 0.8278 (mm) cc_final: 0.7982 (mm) REVERT: E 229 LEU cc_start: 0.8421 (mt) cc_final: 0.8215 (mt) REVERT: E 342 MET cc_start: 0.8424 (ppp) cc_final: 0.7584 (ppp) REVERT: F 26 MET cc_start: 0.7444 (ptt) cc_final: 0.7141 (ptt) REVERT: F 110 ARG cc_start: 0.5143 (OUTLIER) cc_final: 0.4750 (ptt-90) REVERT: F 137 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7053 (pt) REVERT: F 357 PHE cc_start: 0.8089 (t80) cc_final: 0.7443 (t80) REVERT: I 75 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5503 (mmp80) REVERT: I 95 LEU cc_start: 0.4981 (OUTLIER) cc_final: 0.4421 (tt) REVERT: I 679 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7286 (tpt170) REVERT: D 558 LYS cc_start: 0.6234 (mttt) cc_final: 0.5989 (tttt) outliers start: 104 outliers final: 86 residues processed: 282 average time/residue: 0.3608 time to fit residues: 171.5757 Evaluate side-chains 281 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 189 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 319 GLU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 220 CYS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 517 ASP Chi-restraints excluded: chain I residue 547 LYS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 694 HIS Chi-restraints excluded: chain I residue 740 LEU Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 524 ASN Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 349 optimal weight: 30.0000 chunk 230 optimal weight: 3.9990 chunk 371 optimal weight: 40.0000 chunk 226 optimal weight: 0.9990 chunk 176 optimal weight: 30.0000 chunk 258 optimal weight: 20.0000 chunk 389 optimal weight: 0.7980 chunk 358 optimal weight: 30.0000 chunk 310 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 239 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.7624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 27182 Z= 0.327 Angle : 0.732 12.094 37034 Z= 0.381 Chirality : 0.047 0.363 4440 Planarity : 0.005 0.064 4915 Dihedral : 5.578 56.777 4130 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.83 % Favored : 89.12 % Rotamer: Outliers : 5.15 % Allowed : 28.55 % Favored : 66.30 % 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: -2.02 (0.13), residues: 3888 helix: 0.52 (0.14), residues: 1365 sheet: -1.59 (0.19), residues: 734 loop : -2.80 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 610 HIS 0.019 0.002 HIS I 732 PHE 0.024 0.002 PHE F 160 TYR 0.036 0.002 TYR C 660 ARG 0.008 0.001 ARG B 681 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 194 time to evaluate : 4.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 599 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8023 (pttp) REVERT: E 44 ILE cc_start: 0.8566 (tt) cc_final: 0.8172 (tt) REVERT: E 342 MET cc_start: 0.8424 (ppp) cc_final: 0.7613 (ppp) REVERT: F 26 MET cc_start: 0.7478 (ptt) cc_final: 0.7191 (ptt) REVERT: F 110 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.4882 (ptt-90) REVERT: F 137 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7032 (pt) REVERT: F 357 PHE cc_start: 0.8082 (t80) cc_final: 0.7377 (t80) REVERT: F 463 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7369 (tptt) REVERT: I 75 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.5630 (mmp80) REVERT: I 95 LEU cc_start: 0.5231 (OUTLIER) cc_final: 0.4726 (tt) REVERT: I 679 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7246 (tpt170) REVERT: D 558 LYS cc_start: 0.6303 (mttt) cc_final: 0.6013 (tttt) outliers start: 108 outliers final: 92 residues processed: 276 average time/residue: 0.3332 time to fit residues: 155.0987 Evaluate side-chains 289 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 190 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 599 LYS Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 203 TYR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 319 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 220 CYS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 486 ASP Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 290 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 350 ASP Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 517 ASP Chi-restraints excluded: chain I residue 547 LYS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 621 GLN Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 676 ILE Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 694 HIS Chi-restraints excluded: chain I residue 740 LEU Chi-restraints excluded: chain I residue 773 ASP Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 524 ASN Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 190 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 330 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 45 optimal weight: 50.0000 chunk 86 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 319 optimal weight: 0.9990 chunk 39 optimal weight: 50.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** 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 = 0.3975 r_free = 0.3975 target = 0.090250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.076989 restraints weight = 128166.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.077740 restraints weight = 80001.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.078110 restraints weight = 58806.346| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 27182 Z= 0.219 Angle : 0.666 12.390 37034 Z= 0.342 Chirality : 0.045 0.280 4440 Planarity : 0.004 0.064 4915 Dihedral : 5.205 58.335 4130 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.69 % Favored : 91.26 % Rotamer: Outliers : 5.00 % Allowed : 28.74 % Favored : 66.25 % 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: -1.75 (0.13), residues: 3888 helix: 0.81 (0.14), residues: 1363 sheet: -1.46 (0.19), residues: 731 loop : -2.68 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 610 HIS 0.018 0.001 HIS I 732 PHE 0.025 0.002 PHE I 632 TYR 0.035 0.001 TYR C 660 ARG 0.007 0.001 ARG B 681 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4942.08 seconds wall clock time: 91 minutes 17.78 seconds (5477.78 seconds total)