Starting phenix.real_space_refine on Fri Feb 23 09:58:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pl9_13485/02_2024/7pl9_13485_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pl9_13485/02_2024/7pl9_13485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pl9_13485/02_2024/7pl9_13485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pl9_13485/02_2024/7pl9_13485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pl9_13485/02_2024/7pl9_13485_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pl9_13485/02_2024/7pl9_13485_updated.pdb" } resolution = 3.21 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 235 5.16 5 C 24990 2.51 5 N 6305 2.21 5 O 6415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 600": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 827": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A ARG 901": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 987": "NH1" <-> "NH2" Residue "A ARG 1018": "NH1" <-> "NH2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ARG 1093": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 600": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 676": "NH1" <-> "NH2" Residue "B ARG 827": "NH1" <-> "NH2" Residue "B ARG 850": "NH1" <-> "NH2" Residue "B ARG 901": "NH1" <-> "NH2" Residue "B ARG 913": "NH1" <-> "NH2" Residue "B ARG 964": "NH1" <-> "NH2" Residue "B ARG 987": "NH1" <-> "NH2" Residue "B ARG 1018": "NH1" <-> "NH2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B ARG 1093": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 600": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 676": "NH1" <-> "NH2" Residue "C ARG 827": "NH1" <-> "NH2" Residue "C ARG 850": "NH1" <-> "NH2" Residue "C ARG 901": "NH1" <-> "NH2" Residue "C ARG 913": "NH1" <-> "NH2" Residue "C ARG 964": "NH1" <-> "NH2" Residue "C ARG 987": "NH1" <-> "NH2" Residue "C ARG 1018": "NH1" <-> "NH2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C ARG 1093": "NH1" <-> "NH2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D ARG 377": "NH1" <-> "NH2" Residue "D PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 600": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 676": "NH1" <-> "NH2" Residue "D ARG 827": "NH1" <-> "NH2" Residue "D ARG 850": "NH1" <-> "NH2" Residue "D ARG 901": "NH1" <-> "NH2" Residue "D ARG 913": "NH1" <-> "NH2" Residue "D ARG 964": "NH1" <-> "NH2" Residue "D ARG 987": "NH1" <-> "NH2" Residue "D ARG 1018": "NH1" <-> "NH2" Residue "D GLU 1092": "OE1" <-> "OE2" Residue "D ARG 1093": "NH1" <-> "NH2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E ARG 377": "NH1" <-> "NH2" Residue "E PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 600": "NH1" <-> "NH2" Residue "E ARG 628": "NH1" <-> "NH2" Residue "E ARG 676": "NH1" <-> "NH2" Residue "E ARG 827": "NH1" <-> "NH2" Residue "E ARG 850": "NH1" <-> "NH2" Residue "E ARG 901": "NH1" <-> "NH2" Residue "E ARG 913": "NH1" <-> "NH2" Residue "E ARG 964": "NH1" <-> "NH2" Residue "E ARG 987": "NH1" <-> "NH2" Residue "E ARG 1018": "NH1" <-> "NH2" Residue "E GLU 1092": "OE1" <-> "OE2" Residue "E ARG 1093": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37945 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 335 Chain: "B" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 335 Chain: "C" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 335 Chain: "D" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 335 Chain: "E" Number of atoms: 7569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7569 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 962} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 644 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 335 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 18.41, per 1000 atoms: 0.49 Number of scatterers: 37945 At special positions: 0 Unit cell: (184.9, 186.62, 121.26, 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 235 16.00 O 6415 8.00 N 6305 7.00 C 24990 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.32 Conformation dependent library (CDL) restraints added in 6.9 seconds 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 0 sheets defined 70.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.36 Creating SS restraints... Processing helix chain 'A' and resid 67 through 97 removed outlier: 3.565A pdb=" N ILE A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 113 through 140 removed outlier: 4.564A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 158 through 178 removed outlier: 4.199A pdb=" N GLY A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'A' and resid 246 through 274 removed outlier: 5.939A pdb=" N ALA A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 253 " --> pdb=" O TRP A 249 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 311 removed outlier: 4.236A pdb=" N PHE A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 345 removed outlier: 3.978A pdb=" N TRP A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 383 removed outlier: 3.681A pdb=" N GLU A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 490 removed outlier: 4.322A pdb=" N GLU A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 512 through 540 removed outlier: 4.699A pdb=" N HIS A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP A 520 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR A 521 " --> pdb=" O HIS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.564A pdb=" N GLU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 577 removed outlier: 3.636A pdb=" N ILE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 615 removed outlier: 3.536A pdb=" N GLU A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 646 removed outlier: 3.697A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 677 removed outlier: 3.584A pdb=" N LEU A 657 " --> pdb=" O TYR A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 714 removed outlier: 3.562A pdb=" N GLY A 706 " --> pdb=" O TRP A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 723 through 748 removed outlier: 3.696A pdb=" N LYS A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 748 " --> pdb=" O MET A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 839 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 880 through 894 removed outlier: 3.972A pdb=" N ARG A 884 " --> pdb=" O GLU A 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN A 894 " --> pdb=" O ALA A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 907 No H-bonds generated for 'chain 'A' and resid 904 through 907' Processing helix chain 'A' and resid 919 through 936 Processing helix chain 'A' and resid 947 through 996 removed outlier: 3.566A pdb=" N LEU A 952 " --> pdb=" O GLY A 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE A 953 " --> pdb=" O ILE A 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 968 " --> pdb=" O ARG A 964 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 970 " --> pdb=" O GLN A 966 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A 971 " --> pdb=" O ALA A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1020 removed outlier: 3.700A pdb=" N ARG A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS A1019 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1031 Processing helix chain 'A' and resid 1037 through 1043 Processing helix chain 'A' and resid 1049 through 1066 Processing helix chain 'A' and resid 1074 through 1095 removed outlier: 3.722A pdb=" N GLU A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A1087 " --> pdb=" O ALA A1083 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1121 removed outlier: 3.730A pdb=" N VAL A1106 " --> pdb=" O TYR A1102 " (cutoff:3.500A) Proline residue: A1118 - end of helix Processing helix chain 'A' and resid 1127 through 1151 Processing helix chain 'A' and resid 1163 through 1185 removed outlier: 3.530A pdb=" N CYS A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A1168 " --> pdb=" O ASP A1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 97 removed outlier: 3.565A pdb=" N ILE B 88 " --> pdb=" O PHE B 84 " (cutoff:3.500A) Proline residue: B 95 - end of helix Processing helix chain 'B' and resid 113 through 140 removed outlier: 4.564A pdb=" N ILE B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 178 removed outlier: 4.198A pdb=" N GLY B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 216 Processing helix chain 'B' and resid 223 through 243 Processing helix chain 'B' and resid 246 through 274 removed outlier: 5.938A pdb=" N ALA B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE B 253 " --> pdb=" O TRP B 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 311 removed outlier: 4.236A pdb=" N PHE B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 345 removed outlier: 3.978A pdb=" N TRP B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 383 removed outlier: 3.681A pdb=" N GLU B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 490 removed outlier: 4.322A pdb=" N GLU B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' Processing helix chain 'B' and resid 512 through 540 removed outlier: 4.699A pdb=" N HIS B 518 " --> pdb=" O GLY B 514 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 519 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP B 520 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 521 " --> pdb=" O HIS B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 554 removed outlier: 3.563A pdb=" N GLU B 549 " --> pdb=" O PRO B 545 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 577 removed outlier: 3.636A pdb=" N ILE B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 564 " --> pdb=" O GLY B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 615 removed outlier: 3.537A pdb=" N GLU B 603 " --> pdb=" O VAL B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 646 removed outlier: 3.696A pdb=" N VAL B 635 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 677 removed outlier: 3.585A pdb=" N LEU B 657 " --> pdb=" O TYR B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 714 removed outlier: 3.562A pdb=" N GLY B 706 " --> pdb=" O TRP B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 718 No H-bonds generated for 'chain 'B' and resid 716 through 718' Processing helix chain 'B' and resid 723 through 748 removed outlier: 3.696A pdb=" N LYS B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 748 " --> pdb=" O MET B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 839 Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 856 through 866 Processing helix chain 'B' and resid 880 through 894 removed outlier: 3.972A pdb=" N ARG B 884 " --> pdb=" O GLU B 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN B 894 " --> pdb=" O ALA B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 907 No H-bonds generated for 'chain 'B' and resid 904 through 907' Processing helix chain 'B' and resid 919 through 936 Processing helix chain 'B' and resid 947 through 996 removed outlier: 3.566A pdb=" N LEU B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE B 953 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 965 " --> pdb=" O VAL B 961 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 968 " --> pdb=" O ARG B 964 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 970 " --> pdb=" O GLN B 966 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS B 971 " --> pdb=" O ALA B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1020 removed outlier: 3.700A pdb=" N ARG B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B1019 " --> pdb=" O VAL B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1031 Processing helix chain 'B' and resid 1037 through 1043 Processing helix chain 'B' and resid 1049 through 1066 Processing helix chain 'B' and resid 1074 through 1095 removed outlier: 3.722A pdb=" N GLU B1085 " --> pdb=" O ILE B1081 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B1086 " --> pdb=" O LYS B1082 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B1087 " --> pdb=" O ALA B1083 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU B1095 " --> pdb=" O ALA B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1121 removed outlier: 3.729A pdb=" N VAL B1106 " --> pdb=" O TYR B1102 " (cutoff:3.500A) Proline residue: B1118 - end of helix Processing helix chain 'B' and resid 1127 through 1151 Processing helix chain 'B' and resid 1163 through 1185 removed outlier: 3.530A pdb=" N CYS B1167 " --> pdb=" O LEU B1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B1168 " --> pdb=" O ASP B1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B1179 " --> pdb=" O LEU B1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 97 removed outlier: 3.565A pdb=" N ILE C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Proline residue: C 95 - end of helix Processing helix chain 'C' and resid 113 through 140 removed outlier: 4.564A pdb=" N ILE C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 158 through 178 removed outlier: 4.199A pdb=" N GLY C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 216 Processing helix chain 'C' and resid 223 through 243 Processing helix chain 'C' and resid 246 through 274 removed outlier: 5.939A pdb=" N ALA C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 253 " --> pdb=" O TRP C 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 311 removed outlier: 4.236A pdb=" N PHE C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN C 311 " --> pdb=" O MET C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 345 removed outlier: 3.978A pdb=" N TRP C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 383 removed outlier: 3.681A pdb=" N GLU C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 490 removed outlier: 4.322A pdb=" N GLU C 473 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 494 No H-bonds generated for 'chain 'C' and resid 492 through 494' Processing helix chain 'C' and resid 512 through 540 removed outlier: 4.699A pdb=" N HIS C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 519 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR C 521 " --> pdb=" O HIS C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 554 removed outlier: 3.564A pdb=" N GLU C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN C 550 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 577 removed outlier: 3.636A pdb=" N ILE C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 564 " --> pdb=" O GLY C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 615 removed outlier: 3.537A pdb=" N GLU C 603 " --> pdb=" O VAL C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 646 removed outlier: 3.697A pdb=" N VAL C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 636 " --> pdb=" O VAL C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 677 removed outlier: 3.584A pdb=" N LEU C 657 " --> pdb=" O TYR C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 714 removed outlier: 3.562A pdb=" N GLY C 706 " --> pdb=" O TRP C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 718 No H-bonds generated for 'chain 'C' and resid 716 through 718' Processing helix chain 'C' and resid 723 through 748 removed outlier: 3.696A pdb=" N LYS C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C 748 " --> pdb=" O MET C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 839 Processing helix chain 'C' and resid 847 through 852 Processing helix chain 'C' and resid 856 through 866 Processing helix chain 'C' and resid 880 through 894 removed outlier: 3.972A pdb=" N ARG C 884 " --> pdb=" O GLU C 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN C 894 " --> pdb=" O ALA C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 907 No H-bonds generated for 'chain 'C' and resid 904 through 907' Processing helix chain 'C' and resid 919 through 936 Processing helix chain 'C' and resid 947 through 996 removed outlier: 3.566A pdb=" N LEU C 952 " --> pdb=" O GLY C 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE C 953 " --> pdb=" O ILE C 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 968 " --> pdb=" O ARG C 964 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS C 970 " --> pdb=" O GLN C 966 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C 971 " --> pdb=" O ALA C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1020 removed outlier: 3.700A pdb=" N ARG C1005 " --> pdb=" O ALA C1001 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C1019 " --> pdb=" O VAL C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1031 Processing helix chain 'C' and resid 1037 through 1043 Processing helix chain 'C' and resid 1049 through 1066 Processing helix chain 'C' and resid 1074 through 1095 removed outlier: 3.722A pdb=" N GLU C1085 " --> pdb=" O ILE C1081 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C1086 " --> pdb=" O LYS C1082 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C1087 " --> pdb=" O ALA C1083 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C1095 " --> pdb=" O ALA C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1121 removed outlier: 3.729A pdb=" N VAL C1106 " --> pdb=" O TYR C1102 " (cutoff:3.500A) Proline residue: C1118 - end of helix Processing helix chain 'C' and resid 1127 through 1151 Processing helix chain 'C' and resid 1163 through 1185 removed outlier: 3.529A pdb=" N CYS C1167 " --> pdb=" O LEU C1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C1168 " --> pdb=" O ASP C1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP C1179 " --> pdb=" O LEU C1175 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 removed outlier: 3.565A pdb=" N ILE D 88 " --> pdb=" O PHE D 84 " (cutoff:3.500A) Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 113 through 140 removed outlier: 4.565A pdb=" N ILE D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 135 " --> pdb=" O GLY D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 178 removed outlier: 4.198A pdb=" N GLY D 177 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 216 Processing helix chain 'D' and resid 223 through 243 Processing helix chain 'D' and resid 246 through 274 removed outlier: 5.939A pdb=" N ALA D 251 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE D 252 " --> pdb=" O MET D 248 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE D 253 " --> pdb=" O TRP D 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 311 removed outlier: 4.237A pdb=" N PHE D 310 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 345 removed outlier: 3.978A pdb=" N TRP D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 383 removed outlier: 3.681A pdb=" N GLU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 490 removed outlier: 4.321A pdb=" N GLU D 473 " --> pdb=" O ILE D 469 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 494 No H-bonds generated for 'chain 'D' and resid 492 through 494' Processing helix chain 'D' and resid 512 through 540 removed outlier: 4.699A pdb=" N HIS D 518 " --> pdb=" O GLY D 514 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY D 519 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 521 " --> pdb=" O HIS D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 554 removed outlier: 3.564A pdb=" N GLU D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN D 550 " --> pdb=" O ARG D 546 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 577 removed outlier: 3.637A pdb=" N ILE D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 564 " --> pdb=" O GLY D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 615 removed outlier: 3.536A pdb=" N GLU D 603 " --> pdb=" O VAL D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 646 removed outlier: 3.697A pdb=" N VAL D 635 " --> pdb=" O ILE D 631 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 636 " --> pdb=" O VAL D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 677 removed outlier: 3.584A pdb=" N LEU D 657 " --> pdb=" O TYR D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 714 removed outlier: 3.562A pdb=" N GLY D 706 " --> pdb=" O TRP D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 718 No H-bonds generated for 'chain 'D' and resid 716 through 718' Processing helix chain 'D' and resid 723 through 748 removed outlier: 3.697A pdb=" N LYS D 736 " --> pdb=" O ASP D 732 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR D 748 " --> pdb=" O MET D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 839 Processing helix chain 'D' and resid 847 through 852 Processing helix chain 'D' and resid 856 through 866 Processing helix chain 'D' and resid 880 through 894 removed outlier: 3.972A pdb=" N ARG D 884 " --> pdb=" O GLU D 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS D 891 " --> pdb=" O THR D 887 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN D 894 " --> pdb=" O ALA D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 907 No H-bonds generated for 'chain 'D' and resid 904 through 907' Processing helix chain 'D' and resid 919 through 936 Processing helix chain 'D' and resid 947 through 996 removed outlier: 3.566A pdb=" N LEU D 952 " --> pdb=" O GLY D 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE D 953 " --> pdb=" O ILE D 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 965 " --> pdb=" O VAL D 961 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 968 " --> pdb=" O ARG D 964 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 970 " --> pdb=" O GLN D 966 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D 971 " --> pdb=" O ALA D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1020 removed outlier: 3.700A pdb=" N ARG D1005 " --> pdb=" O ALA D1001 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS D1019 " --> pdb=" O VAL D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1031 Processing helix chain 'D' and resid 1037 through 1043 Processing helix chain 'D' and resid 1049 through 1066 Processing helix chain 'D' and resid 1074 through 1095 removed outlier: 3.722A pdb=" N GLU D1085 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D1086 " --> pdb=" O LYS D1082 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER D1087 " --> pdb=" O ALA D1083 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU D1095 " --> pdb=" O ALA D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1121 removed outlier: 3.729A pdb=" N VAL D1106 " --> pdb=" O TYR D1102 " (cutoff:3.500A) Proline residue: D1118 - end of helix Processing helix chain 'D' and resid 1127 through 1151 Processing helix chain 'D' and resid 1163 through 1185 removed outlier: 3.530A pdb=" N CYS D1167 " --> pdb=" O LEU D1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D1168 " --> pdb=" O ASP D1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP D1179 " --> pdb=" O LEU D1175 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 97 removed outlier: 3.564A pdb=" N ILE E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 113 through 140 removed outlier: 4.565A pdb=" N ILE E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 135 " --> pdb=" O GLY E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 154 Processing helix chain 'E' and resid 158 through 178 removed outlier: 4.199A pdb=" N GLY E 177 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 216 Processing helix chain 'E' and resid 223 through 243 Processing helix chain 'E' and resid 246 through 274 removed outlier: 5.938A pdb=" N ALA E 251 " --> pdb=" O TRP E 247 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE E 252 " --> pdb=" O MET E 248 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE E 253 " --> pdb=" O TRP E 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA E 256 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 311 removed outlier: 4.237A pdb=" N PHE E 310 " --> pdb=" O PHE E 306 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN E 311 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 345 removed outlier: 3.978A pdb=" N TRP E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR E 326 " --> pdb=" O GLN E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 383 removed outlier: 3.682A pdb=" N GLU E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E 361 " --> pdb=" O GLN E 357 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY E 362 " --> pdb=" O LYS E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 490 removed outlier: 4.322A pdb=" N GLU E 473 " --> pdb=" O ILE E 469 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 494 No H-bonds generated for 'chain 'E' and resid 492 through 494' Processing helix chain 'E' and resid 512 through 540 removed outlier: 4.699A pdb=" N HIS E 518 " --> pdb=" O GLY E 514 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY E 519 " --> pdb=" O PHE E 515 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP E 520 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR E 521 " --> pdb=" O HIS E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 554 removed outlier: 3.563A pdb=" N GLU E 549 " --> pdb=" O PRO E 545 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN E 550 " --> pdb=" O ARG E 546 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 577 removed outlier: 3.636A pdb=" N ILE E 563 " --> pdb=" O LEU E 559 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA E 564 " --> pdb=" O GLY E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 615 removed outlier: 3.537A pdb=" N GLU E 603 " --> pdb=" O VAL E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 646 removed outlier: 3.697A pdb=" N VAL E 635 " --> pdb=" O ILE E 631 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA E 636 " --> pdb=" O VAL E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 677 removed outlier: 3.584A pdb=" N LEU E 657 " --> pdb=" O TYR E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 714 removed outlier: 3.561A pdb=" N GLY E 706 " --> pdb=" O TRP E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 718 No H-bonds generated for 'chain 'E' and resid 716 through 718' Processing helix chain 'E' and resid 723 through 748 removed outlier: 3.696A pdb=" N LYS E 736 " --> pdb=" O ASP E 732 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR E 748 " --> pdb=" O MET E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 839 Processing helix chain 'E' and resid 847 through 852 Processing helix chain 'E' and resid 856 through 866 Processing helix chain 'E' and resid 880 through 894 removed outlier: 3.973A pdb=" N ARG E 884 " --> pdb=" O GLU E 880 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS E 891 " --> pdb=" O THR E 887 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN E 894 " --> pdb=" O ALA E 890 " (cutoff:3.500A) Processing helix chain 'E' and resid 904 through 907 No H-bonds generated for 'chain 'E' and resid 904 through 907' Processing helix chain 'E' and resid 919 through 936 Processing helix chain 'E' and resid 947 through 996 removed outlier: 3.567A pdb=" N LEU E 952 " --> pdb=" O GLY E 948 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE E 953 " --> pdb=" O ILE E 949 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 965 " --> pdb=" O VAL E 961 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA E 968 " --> pdb=" O ARG E 964 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS E 970 " --> pdb=" O GLN E 966 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS E 971 " --> pdb=" O ALA E 967 " (cutoff:3.500A) Processing helix chain 'E' and resid 1001 through 1020 removed outlier: 3.700A pdb=" N ARG E1005 " --> pdb=" O ALA E1001 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS E1019 " --> pdb=" O VAL E1015 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1031 Processing helix chain 'E' and resid 1037 through 1043 Processing helix chain 'E' and resid 1049 through 1066 Processing helix chain 'E' and resid 1074 through 1095 removed outlier: 3.722A pdb=" N GLU E1085 " --> pdb=" O ILE E1081 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN E1086 " --> pdb=" O LYS E1082 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER E1087 " --> pdb=" O ALA E1083 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU E1095 " --> pdb=" O ALA E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1100 through 1121 removed outlier: 3.730A pdb=" N VAL E1106 " --> pdb=" O TYR E1102 " (cutoff:3.500A) Proline residue: E1118 - end of helix Processing helix chain 'E' and resid 1127 through 1151 Processing helix chain 'E' and resid 1163 through 1185 removed outlier: 3.530A pdb=" N CYS E1167 " --> pdb=" O LEU E1163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E1168 " --> pdb=" O ASP E1164 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP E1179 " --> pdb=" O LEU E1175 " (cutoff:3.500A) 2495 hydrogen bonds defined for protein. 7470 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: 12.71 Time building geometry restraints manager: 15.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11752 1.34 - 1.46: 6783 1.46 - 1.57: 20085 1.57 - 1.69: 0 1.69 - 1.81: 375 Bond restraints: 38995 Sorted by residual: bond pdb=" N ARG E 877 " pdb=" CA ARG E 877 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.40e+00 bond pdb=" N ARG B 877 " pdb=" CA ARG B 877 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.36e+00 bond pdb=" N ARG C 877 " pdb=" CA ARG C 877 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.21e-02 6.83e+03 6.31e+00 bond pdb=" N ARG A 877 " pdb=" CA ARG A 877 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.06e+00 bond pdb=" N ARG D 877 " pdb=" CA ARG D 877 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.21e-02 6.83e+03 5.93e+00 ... (remaining 38990 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.23: 791 106.23 - 113.20: 21590 113.20 - 120.16: 13683 120.16 - 127.13: 16621 127.13 - 134.09: 675 Bond angle restraints: 53360 Sorted by residual: angle pdb=" N GLN B 721 " pdb=" CA GLN B 721 " pdb=" CB GLN B 721 " ideal model delta sigma weight residual 114.17 109.73 4.44 1.14e+00 7.69e-01 1.51e+01 angle pdb=" N GLN D 721 " pdb=" CA GLN D 721 " pdb=" CB GLN D 721 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N GLN A 721 " pdb=" CA GLN A 721 " pdb=" CB GLN A 721 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N GLN E 721 " pdb=" CA GLN E 721 " pdb=" CB GLN E 721 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N GLN C 721 " pdb=" CA GLN C 721 " pdb=" CB GLN C 721 " ideal model delta sigma weight residual 114.17 109.78 4.39 1.14e+00 7.69e-01 1.48e+01 ... (remaining 53355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 20225 17.60 - 35.20: 1715 35.20 - 52.80: 240 52.80 - 70.39: 45 70.39 - 87.99: 10 Dihedral angle restraints: 22235 sinusoidal: 7695 harmonic: 14540 Sorted by residual: dihedral pdb=" CA ARG C 385 " pdb=" C ARG C 385 " pdb=" N VAL C 386 " pdb=" CA VAL C 386 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG E 385 " pdb=" C ARG E 385 " pdb=" N VAL E 386 " pdb=" CA VAL E 386 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG A 385 " pdb=" C ARG A 385 " pdb=" N VAL A 386 " pdb=" CA VAL A 386 " ideal model delta harmonic sigma weight residual 180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 22232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 6165 0.338 - 0.676: 0 0.676 - 1.013: 0 1.013 - 1.351: 0 1.351 - 1.689: 10 Chirality restraints: 6175 Sorted by residual: chirality pdb=" CG LEU D 323 " pdb=" CB LEU D 323 " pdb=" CD1 LEU D 323 " pdb=" CD2 LEU D 323 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" CG LEU E 323 " pdb=" CB LEU E 323 " pdb=" CD1 LEU E 323 " pdb=" CD2 LEU E 323 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" CG LEU A 323 " pdb=" CB LEU A 323 " pdb=" CD1 LEU A 323 " pdb=" CD2 LEU A 323 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 ... (remaining 6172 not shown) Planarity restraints: 6565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C1071 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO C1072 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C1072 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C1072 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1071 " -0.035 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO B1072 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B1072 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B1072 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1071 " -0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A1072 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A1072 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1072 " -0.029 5.00e-02 4.00e+02 ... (remaining 6562 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5113 2.75 - 3.29: 40604 3.29 - 3.82: 62372 3.82 - 4.36: 67256 4.36 - 4.90: 118039 Nonbonded interactions: 293384 Sorted by model distance: nonbonded pdb=" OD1 ASP B 829 " pdb=" OG SER B 832 " model vdw 2.209 2.440 nonbonded pdb=" OD1 ASP E 829 " pdb=" OG SER E 832 " model vdw 2.209 2.440 nonbonded pdb=" OD1 ASP C 829 " pdb=" OG SER C 832 " model vdw 2.209 2.440 nonbonded pdb=" OD1 ASP A 829 " pdb=" OG SER A 832 " model vdw 2.209 2.440 nonbonded pdb=" OD1 ASP D 829 " pdb=" OG SER D 832 " model vdw 2.210 2.440 ... (remaining 293379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.030 Extract box with map and model: 16.010 Check model and map are aligned: 0.580 Set scattering table: 0.320 Process input model: 94.080 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.006 0.051 38995 Z= 0.382 Angle : 0.682 10.599 53360 Z= 0.398 Chirality : 0.079 1.689 6175 Planarity : 0.004 0.052 6565 Dihedral : 13.260 87.993 12815 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.10), residues: 4930 helix: -1.64 (0.07), residues: 3475 sheet: None (None), residues: 0 loop : -3.20 (0.13), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 520 HIS 0.005 0.001 HIS E1105 PHE 0.019 0.001 PHE C1109 TYR 0.023 0.002 TYR D 637 ARG 0.005 0.000 ARG C1018 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 4.311 Fit side-chains REVERT: A 229 VAL cc_start: 0.8190 (m) cc_final: 0.7960 (p) REVERT: A 332 MET cc_start: 0.7217 (ttp) cc_final: 0.7014 (ttt) REVERT: A 627 PHE cc_start: 0.5705 (m-10) cc_final: 0.5119 (m-80) REVERT: E 263 LEU cc_start: 0.7557 (mt) cc_final: 0.7325 (mt) REVERT: E 332 MET cc_start: 0.7404 (ttp) cc_final: 0.7188 (ttt) REVERT: E 334 LEU cc_start: 0.8178 (mm) cc_final: 0.7960 (mt) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.4511 time to fit residues: 514.9043 Evaluate side-chains 409 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 4.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 417 optimal weight: 20.0000 chunk 375 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 387 optimal weight: 0.1980 chunk 150 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 chunk 449 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 819 ASN E 819 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38995 Z= 0.184 Angle : 0.535 9.858 53360 Z= 0.284 Chirality : 0.038 0.148 6175 Planarity : 0.004 0.048 6565 Dihedral : 4.596 44.855 5375 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.49 % Allowed : 9.12 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 4930 helix: 0.74 (0.08), residues: 3530 sheet: None (None), residues: 0 loop : -2.32 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 258 HIS 0.003 0.001 HIS C 617 PHE 0.026 0.001 PHE B1109 TYR 0.029 0.001 TYR C 637 ARG 0.005 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 470 time to evaluate : 4.230 Fit side-chains REVERT: A 229 VAL cc_start: 0.8300 (m) cc_final: 0.8027 (p) REVERT: A 332 MET cc_start: 0.7354 (ttp) cc_final: 0.7081 (ttt) REVERT: A 354 VAL cc_start: 0.6867 (m) cc_final: 0.6652 (t) REVERT: B 130 GLU cc_start: 0.7470 (mp0) cc_final: 0.7162 (mp0) REVERT: B 354 VAL cc_start: 0.7302 (m) cc_final: 0.7074 (t) REVERT: C 130 GLU cc_start: 0.7515 (mp0) cc_final: 0.7299 (mp0) REVERT: C 229 VAL cc_start: 0.8439 (m) cc_final: 0.8209 (p) REVERT: C 735 MET cc_start: 0.6678 (ttm) cc_final: 0.6276 (ttt) REVERT: D 354 VAL cc_start: 0.6979 (m) cc_final: 0.6773 (t) REVERT: D 523 MET cc_start: 0.7464 (tpp) cc_final: 0.7204 (tpp) REVERT: E 332 MET cc_start: 0.7532 (ttp) cc_final: 0.7294 (ttt) outliers start: 54 outliers final: 31 residues processed: 501 average time/residue: 0.4432 time to fit residues: 378.3599 Evaluate side-chains 430 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 399 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 579 ASN Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 602 MET Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 827 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 249 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 374 optimal weight: 0.7980 chunk 306 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 450 optimal weight: 0.7980 chunk 486 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 446 optimal weight: 10.0000 chunk 153 optimal weight: 0.0470 chunk 361 optimal weight: 10.0000 overall best weight: 2.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN D1023 ASN E 819 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 38995 Z= 0.240 Angle : 0.549 7.455 53360 Z= 0.293 Chirality : 0.040 0.177 6175 Planarity : 0.004 0.051 6565 Dihedral : 4.405 36.479 5375 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.62 % Allowed : 12.95 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.12), residues: 4930 helix: 1.58 (0.09), residues: 3535 sheet: None (None), residues: 0 loop : -1.91 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 728 HIS 0.002 0.001 HIS B 849 PHE 0.038 0.002 PHE A1109 TYR 0.024 0.001 TYR B 234 ARG 0.003 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 467 time to evaluate : 4.721 Fit side-chains REVERT: A 229 VAL cc_start: 0.8373 (m) cc_final: 0.8133 (p) REVERT: A 332 MET cc_start: 0.7415 (ttp) cc_final: 0.7156 (ttt) REVERT: A 354 VAL cc_start: 0.6900 (m) cc_final: 0.6696 (t) REVERT: C 123 MET cc_start: 0.7547 (tpp) cc_final: 0.7343 (mmm) REVERT: C 130 GLU cc_start: 0.7454 (mp0) cc_final: 0.7191 (mp0) REVERT: C 229 VAL cc_start: 0.8473 (m) cc_final: 0.8255 (p) REVERT: C 735 MET cc_start: 0.6825 (ttm) cc_final: 0.6376 (ttt) REVERT: D 354 VAL cc_start: 0.7212 (m) cc_final: 0.7011 (t) REVERT: D 523 MET cc_start: 0.7570 (tpp) cc_final: 0.7277 (tpp) REVERT: E 307 MET cc_start: 0.7183 (ttp) cc_final: 0.6818 (tmm) outliers start: 95 outliers final: 70 residues processed: 534 average time/residue: 0.4326 time to fit residues: 400.9161 Evaluate side-chains 464 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 394 time to evaluate : 4.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 579 ASN Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 985 MET Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 602 MET Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 827 ARG Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 1087 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 444 optimal weight: 4.9990 chunk 338 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 302 optimal weight: 20.0000 chunk 451 optimal weight: 0.0980 chunk 478 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 428 optimal weight: 0.0970 chunk 128 optimal weight: 5.9990 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN A1004 ASN B 336 HIS B 554 GLN B1004 ASN C1004 ASN C1020 HIS D1004 ASN E 336 HIS E 550 ASN E1004 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 38995 Z= 0.270 Angle : 0.563 9.297 53360 Z= 0.296 Chirality : 0.040 0.174 6175 Planarity : 0.004 0.050 6565 Dihedral : 4.374 33.160 5375 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.09 % Allowed : 15.15 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.20 (0.12), residues: 4930 helix: 1.74 (0.09), residues: 3555 sheet: None (None), residues: 0 loop : -1.81 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 728 HIS 0.003 0.001 HIS E 849 PHE 0.033 0.001 PHE B1109 TYR 0.021 0.001 TYR B 234 ARG 0.003 0.000 ARG B1093 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 446 time to evaluate : 4.465 Fit side-chains REVERT: A 229 VAL cc_start: 0.8307 (m) cc_final: 0.8058 (p) REVERT: A 381 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7087 (ttm170) REVERT: A 653 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.5941 (t80) REVERT: B 653 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.7002 (t80) REVERT: B 735 MET cc_start: 0.7213 (ttm) cc_final: 0.6949 (ttm) REVERT: C 123 MET cc_start: 0.7641 (tpp) cc_final: 0.7414 (mmm) REVERT: C 130 GLU cc_start: 0.7553 (mp0) cc_final: 0.7315 (mp0) REVERT: C 229 VAL cc_start: 0.8497 (m) cc_final: 0.8276 (p) REVERT: C 258 TRP cc_start: 0.4927 (OUTLIER) cc_final: 0.4616 (m100) REVERT: C 735 MET cc_start: 0.6744 (ttm) cc_final: 0.6333 (ttm) REVERT: D 523 MET cc_start: 0.7632 (tpp) cc_final: 0.7339 (tpp) REVERT: E 307 MET cc_start: 0.7113 (ttp) cc_final: 0.6751 (tmm) REVERT: E 653 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6083 (t80) outliers start: 112 outliers final: 84 residues processed: 524 average time/residue: 0.4356 time to fit residues: 391.9971 Evaluate side-chains 487 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 398 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 579 ASN Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 652 TRP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 985 MET Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 904 MET Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 602 MET Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 827 ARG Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1120 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 398 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 356 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 408 optimal weight: 50.0000 chunk 330 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 244 optimal weight: 0.6980 chunk 429 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS A 550 ASN A1004 ASN C 554 GLN D 554 GLN D1004 ASN E 550 ASN E1004 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 38995 Z= 0.307 Angle : 0.582 7.485 53360 Z= 0.308 Chirality : 0.041 0.182 6175 Planarity : 0.004 0.051 6565 Dihedral : 4.427 31.256 5375 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.02 % Allowed : 16.50 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.17 (0.12), residues: 4930 helix: 1.74 (0.09), residues: 3550 sheet: None (None), residues: 0 loop : -1.84 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 728 HIS 0.003 0.001 HIS A 849 PHE 0.041 0.002 PHE A1109 TYR 0.021 0.002 TYR A 637 ARG 0.003 0.000 ARG E 827 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 420 time to evaluate : 4.141 Fit side-chains REVERT: A 123 MET cc_start: 0.7583 (tpp) cc_final: 0.7272 (mmm) REVERT: A 229 VAL cc_start: 0.8245 (m) cc_final: 0.7979 (p) REVERT: A 381 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7120 (ttm170) REVERT: A 653 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.5858 (t80) REVERT: B 176 MET cc_start: 0.6914 (mmm) cc_final: 0.6475 (mmm) REVERT: B 381 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7266 (ttm170) REVERT: B 653 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6959 (t80) REVERT: B 735 MET cc_start: 0.7181 (ttm) cc_final: 0.6891 (ttm) REVERT: C 123 MET cc_start: 0.7676 (tpp) cc_final: 0.7424 (mmm) REVERT: C 130 GLU cc_start: 0.7541 (mp0) cc_final: 0.7289 (mp0) REVERT: C 229 VAL cc_start: 0.8518 (m) cc_final: 0.8300 (p) REVERT: C 258 TRP cc_start: 0.5089 (OUTLIER) cc_final: 0.4732 (m100) REVERT: C 381 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7324 (ttm170) REVERT: D 176 MET cc_start: 0.6702 (mmp) cc_final: 0.6462 (mmm) REVERT: D 381 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7343 (ttm170) REVERT: D 523 MET cc_start: 0.7665 (tpp) cc_final: 0.7386 (tpp) REVERT: E 130 GLU cc_start: 0.7557 (mp0) cc_final: 0.7160 (mp0) REVERT: E 307 MET cc_start: 0.7131 (ttp) cc_final: 0.6795 (tmm) REVERT: E 381 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7305 (ttm170) REVERT: E 653 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6109 (t80) REVERT: E 937 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6608 (t80) outliers start: 146 outliers final: 108 residues processed: 534 average time/residue: 0.4453 time to fit residues: 407.3446 Evaluate side-chains 509 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 391 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 652 TRP Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 579 ASN Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 985 MET Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 586 VAL Chi-restraints excluded: chain E residue 602 MET Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 827 ARG Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 929 ILE Chi-restraints excluded: chain E residue 937 PHE Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1169 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 160 optimal weight: 0.0670 chunk 430 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 478 optimal weight: 0.9980 chunk 397 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS A 550 ASN A1004 ASN A1020 HIS B 739 HIS D1004 ASN E1004 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 38995 Z= 0.180 Angle : 0.502 8.158 53360 Z= 0.263 Chirality : 0.038 0.162 6175 Planarity : 0.004 0.051 6565 Dihedral : 4.181 33.820 5375 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.50 % Allowed : 18.40 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.54 (0.12), residues: 4930 helix: 2.01 (0.09), residues: 3530 sheet: None (None), residues: 0 loop : -1.67 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 728 HIS 0.010 0.000 HIS A 375 PHE 0.036 0.001 PHE C1109 TYR 0.023 0.001 TYR D 637 ARG 0.004 0.000 ARG D 864 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 422 time to evaluate : 4.633 Fit side-chains REVERT: A 123 MET cc_start: 0.7428 (tpp) cc_final: 0.7176 (mmm) REVERT: A 229 VAL cc_start: 0.8237 (m) cc_final: 0.7977 (p) REVERT: A 381 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7080 (ttm170) REVERT: A 653 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.5900 (t80) REVERT: B 123 MET cc_start: 0.7626 (tpp) cc_final: 0.7269 (mmm) REVERT: B 268 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7114 (t80) REVERT: B 307 MET cc_start: 0.7004 (ttp) cc_final: 0.6693 (tmm) REVERT: B 381 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7142 (ttm170) REVERT: B 653 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6635 (t80) REVERT: B 735 MET cc_start: 0.7163 (ttm) cc_final: 0.6814 (ttm) REVERT: C 229 VAL cc_start: 0.8466 (m) cc_final: 0.8230 (p) REVERT: C 258 TRP cc_start: 0.4989 (OUTLIER) cc_final: 0.4731 (m100) REVERT: C 307 MET cc_start: 0.7232 (ttp) cc_final: 0.7006 (tmm) REVERT: C 381 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7213 (ttm170) REVERT: D 381 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7232 (ttm170) REVERT: D 523 MET cc_start: 0.7655 (tpp) cc_final: 0.7409 (tpp) REVERT: E 307 MET cc_start: 0.7178 (ttp) cc_final: 0.6911 (tmm) REVERT: E 381 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7193 (ttm170) REVERT: E 653 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6246 (t80) REVERT: E 937 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6490 (t80) outliers start: 127 outliers final: 96 residues processed: 521 average time/residue: 0.4426 time to fit residues: 395.8738 Evaluate side-chains 496 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 389 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 579 ASN Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 985 MET Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 904 MET Chi-restraints excluded: chain D residue 937 PHE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 602 MET Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 827 ARG Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 937 PHE Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1183 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 461 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 272 optimal weight: 0.0980 chunk 349 optimal weight: 0.9980 chunk 270 optimal weight: 9.9990 chunk 403 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 477 optimal weight: 0.7980 chunk 298 optimal weight: 8.9990 chunk 290 optimal weight: 0.8980 chunk 220 optimal weight: 30.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN A1004 ASN D1004 ASN E1004 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38995 Z= 0.169 Angle : 0.493 11.073 53360 Z= 0.256 Chirality : 0.037 0.168 6175 Planarity : 0.004 0.050 6565 Dihedral : 4.002 32.559 5375 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.61 % Allowed : 18.84 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.80 (0.12), residues: 4930 helix: 2.24 (0.09), residues: 3500 sheet: None (None), residues: 0 loop : -1.59 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 728 HIS 0.002 0.000 HIS C1105 PHE 0.036 0.001 PHE C1109 TYR 0.022 0.001 TYR D 637 ARG 0.004 0.000 ARG D 864 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 418 time to evaluate : 4.260 Fit side-chains REVERT: A 229 VAL cc_start: 0.8285 (m) cc_final: 0.8020 (p) REVERT: A 653 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.5783 (t80) REVERT: B 268 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7114 (t80) REVERT: B 307 MET cc_start: 0.6943 (ttp) cc_final: 0.6623 (tmm) REVERT: B 381 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7123 (ttm170) REVERT: B 653 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6347 (t80) REVERT: B 735 MET cc_start: 0.7152 (ttm) cc_final: 0.6710 (ttm) REVERT: C 123 MET cc_start: 0.7365 (tpp) cc_final: 0.6978 (mmm) REVERT: C 130 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7184 (mp0) REVERT: C 176 MET cc_start: 0.6765 (mmm) cc_final: 0.6462 (mmm) REVERT: C 229 VAL cc_start: 0.8526 (m) cc_final: 0.8292 (p) REVERT: C 258 TRP cc_start: 0.4932 (OUTLIER) cc_final: 0.4633 (m100) REVERT: C 307 MET cc_start: 0.7247 (ttp) cc_final: 0.6993 (tmm) REVERT: C 381 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7175 (ttm170) REVERT: C 879 TRP cc_start: 0.5316 (m-90) cc_final: 0.5100 (m-90) REVERT: D 381 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7186 (ttm170) REVERT: D 523 MET cc_start: 0.7600 (tpp) cc_final: 0.7368 (tpp) REVERT: D 737 LEU cc_start: 0.7834 (tp) cc_final: 0.7268 (mt) REVERT: E 307 MET cc_start: 0.7180 (ttp) cc_final: 0.6923 (tmm) REVERT: E 638 MET cc_start: 0.6961 (tpp) cc_final: 0.6666 (tpp) REVERT: E 653 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6139 (t80) REVERT: E 735 MET cc_start: 0.7381 (tmm) cc_final: 0.7155 (tmm) REVERT: E 937 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6366 (t80) outliers start: 131 outliers final: 100 residues processed: 517 average time/residue: 0.4487 time to fit residues: 398.5099 Evaluate side-chains 503 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 394 time to evaluate : 4.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 579 ASN Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 985 MET Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 904 MET Chi-restraints excluded: chain D residue 937 PHE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 602 MET Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 827 ARG Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 937 PHE Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1183 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 295 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 303 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 235 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 375 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A1004 ASN D1004 ASN E1004 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38995 Z= 0.147 Angle : 0.475 7.493 53360 Z= 0.246 Chirality : 0.037 0.168 6175 Planarity : 0.003 0.049 6565 Dihedral : 3.897 32.631 5375 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.50 % Allowed : 19.42 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.93 (0.12), residues: 4930 helix: 2.35 (0.09), residues: 3495 sheet: None (None), residues: 0 loop : -1.57 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 728 HIS 0.002 0.000 HIS C1105 PHE 0.033 0.001 PHE C1109 TYR 0.021 0.001 TYR D 637 ARG 0.003 0.000 ARG D1005 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 415 time to evaluate : 4.285 Fit side-chains REVERT: A 123 MET cc_start: 0.7176 (tpp) cc_final: 0.6963 (mmm) REVERT: A 229 VAL cc_start: 0.8256 (m) cc_final: 0.7979 (p) REVERT: A 307 MET cc_start: 0.7162 (ttp) cc_final: 0.6887 (tmm) REVERT: A 653 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.5823 (t80) REVERT: B 123 MET cc_start: 0.7349 (tpp) cc_final: 0.7135 (mmm) REVERT: B 268 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7089 (t80) REVERT: B 307 MET cc_start: 0.6958 (ttp) cc_final: 0.6646 (tmm) REVERT: B 381 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7094 (ttm170) REVERT: B 653 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6339 (t80) REVERT: B 735 MET cc_start: 0.7140 (ttm) cc_final: 0.6649 (ttm) REVERT: B 737 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7794 (tp) REVERT: B 753 VAL cc_start: 0.6273 (OUTLIER) cc_final: 0.5406 (m) REVERT: C 91 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6958 (tt) REVERT: C 229 VAL cc_start: 0.8551 (m) cc_final: 0.8312 (p) REVERT: C 258 TRP cc_start: 0.4839 (OUTLIER) cc_final: 0.4557 (m100) REVERT: C 307 MET cc_start: 0.7295 (ttp) cc_final: 0.7029 (tmm) REVERT: C 381 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7139 (ttm170) REVERT: C 638 MET cc_start: 0.6929 (tpp) cc_final: 0.6395 (tpp) REVERT: C 879 TRP cc_start: 0.5399 (m-10) cc_final: 0.5179 (m-90) REVERT: D 381 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7108 (ttm170) REVERT: D 737 LEU cc_start: 0.7592 (tp) cc_final: 0.7152 (mt) REVERT: E 307 MET cc_start: 0.7085 (ttp) cc_final: 0.6867 (tmm) REVERT: E 653 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6162 (t80) REVERT: E 735 MET cc_start: 0.7362 (tmm) cc_final: 0.7145 (tmm) REVERT: E 937 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6333 (t80) outliers start: 127 outliers final: 97 residues processed: 509 average time/residue: 0.4675 time to fit residues: 405.4667 Evaluate side-chains 500 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 391 time to evaluate : 4.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 985 MET Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 904 MET Chi-restraints excluded: chain D residue 937 PHE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 523 MET Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 602 MET Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 827 ARG Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 937 PHE Chi-restraints excluded: chain E residue 1087 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 434 optimal weight: 10.0000 chunk 457 optimal weight: 0.0970 chunk 417 optimal weight: 0.8980 chunk 444 optimal weight: 9.9990 chunk 456 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 349 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 401 optimal weight: 20.0000 chunk 420 optimal weight: 4.9990 overall best weight: 1.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A1004 ASN C 579 ASN D1004 ASN E1004 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38995 Z= 0.167 Angle : 0.491 11.406 53360 Z= 0.253 Chirality : 0.037 0.168 6175 Planarity : 0.003 0.049 6565 Dihedral : 3.888 32.123 5375 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.36 % Allowed : 19.97 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.93 (0.12), residues: 4930 helix: 2.32 (0.09), residues: 3505 sheet: None (None), residues: 0 loop : -1.50 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 728 HIS 0.002 0.000 HIS C1105 PHE 0.035 0.001 PHE C1109 TYR 0.020 0.001 TYR D 637 ARG 0.002 0.000 ARG B 835 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 406 time to evaluate : 4.438 Fit side-chains REVERT: A 258 TRP cc_start: 0.6097 (m100) cc_final: 0.5801 (m100) REVERT: A 307 MET cc_start: 0.7182 (ttp) cc_final: 0.6912 (tmm) REVERT: A 653 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.5831 (t80) REVERT: B 123 MET cc_start: 0.7378 (tpp) cc_final: 0.7170 (mmm) REVERT: B 268 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7126 (t80) REVERT: B 307 MET cc_start: 0.6982 (ttp) cc_final: 0.6675 (tmm) REVERT: B 381 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7089 (ttm170) REVERT: B 653 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6287 (t80) REVERT: B 735 MET cc_start: 0.7078 (ttm) cc_final: 0.6860 (tmm) REVERT: B 1187 GLN cc_start: 0.5052 (OUTLIER) cc_final: 0.4669 (pm20) REVERT: C 91 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6986 (tt) REVERT: C 130 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7224 (mp0) REVERT: C 229 VAL cc_start: 0.8542 (m) cc_final: 0.8303 (p) REVERT: C 258 TRP cc_start: 0.4935 (OUTLIER) cc_final: 0.4606 (m100) REVERT: C 307 MET cc_start: 0.7288 (ttp) cc_final: 0.6997 (tmm) REVERT: C 381 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7168 (ttm170) REVERT: C 879 TRP cc_start: 0.5434 (m-10) cc_final: 0.5204 (m-90) REVERT: D 381 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7113 (ttm170) REVERT: D 737 LEU cc_start: 0.7528 (tp) cc_final: 0.7296 (mt) REVERT: E 307 MET cc_start: 0.7106 (ttp) cc_final: 0.6889 (tmm) REVERT: E 381 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7113 (ttm170) REVERT: E 638 MET cc_start: 0.6976 (tpp) cc_final: 0.6671 (tpp) REVERT: E 653 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6099 (t80) REVERT: E 735 MET cc_start: 0.7376 (tmm) cc_final: 0.7159 (tmm) REVERT: E 937 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.6350 (t80) outliers start: 122 outliers final: 106 residues processed: 495 average time/residue: 0.4344 time to fit residues: 367.3512 Evaluate side-chains 517 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 399 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1187 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 115 TYR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 579 ASN Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 985 MET Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 904 MET Chi-restraints excluded: chain D residue 937 PHE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 523 MET Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 602 MET Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 827 ARG Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 937 PHE Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1183 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 443 optimal weight: 3.9990 chunk 291 optimal weight: 0.6980 chunk 470 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 326 optimal weight: 6.9990 chunk 493 optimal weight: 2.9990 chunk 453 optimal weight: 5.9990 chunk 392 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 303 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A1004 ASN C 579 ASN E1004 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38995 Z= 0.174 Angle : 0.502 15.575 53360 Z= 0.257 Chirality : 0.038 0.178 6175 Planarity : 0.004 0.049 6565 Dihedral : 3.910 32.383 5375 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.36 % Allowed : 20.11 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.93 (0.12), residues: 4930 helix: 2.31 (0.09), residues: 3505 sheet: None (None), residues: 0 loop : -1.49 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 728 HIS 0.002 0.000 HIS A 375 PHE 0.036 0.001 PHE C1109 TYR 0.020 0.001 TYR A 637 ARG 0.002 0.000 ARG B 835 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 405 time to evaluate : 4.775 Fit side-chains REVERT: A 123 MET cc_start: 0.7031 (tpp) cc_final: 0.6810 (mmm) REVERT: A 258 TRP cc_start: 0.6080 (m100) cc_final: 0.5788 (m100) REVERT: A 307 MET cc_start: 0.7248 (ttp) cc_final: 0.6982 (tmm) REVERT: A 653 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.5779 (t80) REVERT: B 123 MET cc_start: 0.7387 (tpp) cc_final: 0.7176 (mmm) REVERT: B 268 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7212 (t80) REVERT: B 307 MET cc_start: 0.6990 (ttp) cc_final: 0.6684 (tmm) REVERT: B 381 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7073 (ttm170) REVERT: B 653 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6235 (t80) REVERT: B 735 MET cc_start: 0.7075 (ttm) cc_final: 0.6864 (tmm) REVERT: B 1187 GLN cc_start: 0.5068 (OUTLIER) cc_final: 0.4653 (pm20) REVERT: C 91 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6985 (tt) REVERT: C 130 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7294 (mp0) REVERT: C 229 VAL cc_start: 0.8532 (m) cc_final: 0.8291 (p) REVERT: C 258 TRP cc_start: 0.4916 (OUTLIER) cc_final: 0.4598 (m100) REVERT: C 381 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7150 (ttm170) REVERT: C 638 MET cc_start: 0.6979 (tpp) cc_final: 0.6661 (tpp) REVERT: C 879 TRP cc_start: 0.5451 (m-10) cc_final: 0.5192 (m-90) REVERT: D 381 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7137 (ttm170) REVERT: D 708 LEU cc_start: 0.7125 (tp) cc_final: 0.6925 (tp) REVERT: D 737 LEU cc_start: 0.7773 (tp) cc_final: 0.7286 (mt) REVERT: E 307 MET cc_start: 0.7176 (ttp) cc_final: 0.6946 (tmm) REVERT: E 381 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7099 (ttm170) REVERT: E 638 MET cc_start: 0.6961 (tpp) cc_final: 0.6698 (tpp) REVERT: E 653 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6123 (t80) REVERT: E 735 MET cc_start: 0.7387 (tmm) cc_final: 0.7158 (tmm) REVERT: E 937 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6360 (t80) outliers start: 122 outliers final: 108 residues processed: 495 average time/residue: 0.4424 time to fit residues: 374.6395 Evaluate side-chains 520 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 400 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1187 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 115 TYR Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 268 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 579 ASN Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 985 MET Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 302 TYR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 893 ILE Chi-restraints excluded: chain D residue 904 MET Chi-restraints excluded: chain D residue 937 PHE Chi-restraints excluded: chain D residue 1087 SER Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain E residue 120 TRP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 523 MET Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 602 MET Chi-restraints excluded: chain E residue 653 TYR Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 827 ARG Chi-restraints excluded: chain E residue 842 GLN Chi-restraints excluded: chain E residue 893 ILE Chi-restraints excluded: chain E residue 904 MET Chi-restraints excluded: chain E residue 937 PHE Chi-restraints excluded: chain E residue 1087 SER Chi-restraints excluded: chain E residue 1183 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 240 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 418 optimal weight: 0.0570 chunk 120 optimal weight: 3.9990 chunk 362 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 393 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 403 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A1004 ASN C 579 ASN D1004 ASN E1004 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.168158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114315 restraints weight = 64868.473| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.11 r_work: 0.3234 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 38995 Z= 0.154 Angle : 0.491 13.808 53360 Z= 0.251 Chirality : 0.037 0.170 6175 Planarity : 0.003 0.047 6565 Dihedral : 3.853 33.772 5375 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.36 % Allowed : 20.41 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.97 (0.12), residues: 4930 helix: 2.37 (0.09), residues: 3490 sheet: None (None), residues: 0 loop : -1.51 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 728 HIS 0.002 0.000 HIS C1105 PHE 0.034 0.001 PHE C1109 TYR 0.020 0.001 TYR A 637 ARG 0.002 0.000 ARG B 835 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9513.32 seconds wall clock time: 171 minutes 12.64 seconds (10272.64 seconds total)