Starting phenix.real_space_refine on Tue Feb 20 13:54:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vya_32198/02_2024/7vya_32198_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vya_32198/02_2024/7vya_32198.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vya_32198/02_2024/7vya_32198_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vya_32198/02_2024/7vya_32198_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vya_32198/02_2024/7vya_32198_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vya_32198/02_2024/7vya_32198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vya_32198/02_2024/7vya_32198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vya_32198/02_2024/7vya_32198_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vya_32198/02_2024/7vya_32198_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 188 5.16 5 C 17737 2.51 5 N 4885 2.21 5 O 5180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 346": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 118": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 716": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 246": "OE1" <-> "OE2" Residue "Q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28031 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2359 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3044 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 20, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'PEE': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 48.135 48.231 104.012 1.00 12.56 S ATOM 3048 SG CYS A 425 47.684 44.741 109.630 1.00 17.81 S ATOM 2726 SG CYS A 385 44.694 44.054 104.264 1.00 15.03 S ATOM 2687 SG CYS A 379 43.290 49.265 108.324 1.00 16.08 S ATOM 3949 SG CYS B 113 36.031 65.527 70.194 1.00 28.65 S ATOM 3968 SG CYS B 116 40.983 62.336 73.518 1.00 28.65 S ATOM 3991 SG CYS B 119 41.999 65.050 68.063 1.00 28.65 S ATOM 4320 SG CYS B 162 38.734 59.572 69.013 1.00 28.65 S ATOM 4018 SG CYS B 123 48.013 67.124 62.940 1.00 28.65 S ATOM 4244 SG CYS B 152 45.437 65.605 57.208 1.00 28.65 S ATOM 4291 SG CYS B 158 43.527 62.202 62.185 1.00 28.65 S ATOM 4270 SG CYS B 155 49.463 61.689 60.200 1.00 28.65 S ATOM 5712 SG CYS C 166 51.494 64.825 52.598 1.00 28.65 S ATOM 4984 SG CYS C 72 52.083 66.338 46.238 1.00 11.08 S ATOM 4978 SG CYS C 71 55.883 63.591 48.118 1.00 11.39 S ATOM 5482 SG CYS C 136 54.475 69.342 50.815 1.00 20.64 S ATOM 14538 SG CYS M 131 41.257 62.515 85.622 1.00 22.94 S ATOM 14517 SG CYS M 128 44.137 57.602 82.293 1.00 28.65 S ATOM 14578 SG CYS M 137 46.954 60.853 87.303 1.00 15.42 S ATOM 14910 SG CYS M 179 46.350 61.045 98.459 1.00 28.65 S ATOM 15264 SG CYS M 226 43.154 63.984 94.451 1.00 19.45 S ATOM 14934 SG CYS M 182 41.404 64.206 100.637 1.00 28.65 S ATOM 14887 SG CYS M 176 40.274 58.774 97.266 1.00 20.94 S ATOM 14135 SG CYS M 78 57.481 54.944 101.112 1.00 17.45 S ATOM 14236 SG CYS M 92 56.120 57.041 103.627 1.00 12.00 S ATOM 14024 SG CYS M 64 51.680 57.676 101.842 1.00 28.65 S ATOM 14110 SG CYS M 75 52.145 55.742 98.654 1.00 16.94 S ATOM 21073 SG CYS O 135 31.016 32.726 113.102 1.00 47.88 S ATOM 21107 SG CYS O 140 30.663 29.379 114.101 1.00 50.11 S ATOM 21387 SG CYS O 176 35.692 33.871 115.533 1.00 48.14 S ATOM 21410 SG CYS O 180 35.480 30.182 115.933 1.00 57.41 S ATOM 27168 SG CYS T 86 27.929 52.911 78.535 1.00 15.04 S ATOM 27346 SG CYS T 111 29.451 56.281 79.491 1.00 16.86 S Time building chain proxies: 14.30, per 1000 atoms: 0.51 Number of scatterers: 28031 At special positions: 0 Unit cell: (122.459, 137.498, 158.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 188 16.00 P 11 15.00 Mg 1 11.99 O 5180 8.00 N 4885 7.00 C 17737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.46 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 25 sheets defined 38.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.520A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.567A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.043A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.571A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.921A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 111 through 123 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.113A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 107 removed outlier: 4.322A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.929A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 137 removed outlier: 5.250A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.923A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.069A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.911A pdb=" N HIS J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG J 95 " --> pdb=" O THR J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 218 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 322 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 355 removed outlier: 4.671A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 removed outlier: 3.937A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.534A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 No H-bonds generated for 'chain 'L' and resid 62 through 65' Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 120 through 123 removed outlier: 4.490A pdb=" N ASN L 123 " --> pdb=" O PRO L 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 120 through 123' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.834A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.064A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.654A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 361 removed outlier: 3.716A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 390 through 395 removed outlier: 3.615A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 395' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 425 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 4.000A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.745A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 143 removed outlier: 3.816A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.700A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix removed outlier: 3.570A pdb=" N THR P 98 " --> pdb=" O PRO P 95 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU P 100 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG P 101 " --> pdb=" O THR P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.908A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.688A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 4.117A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.213A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.037A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 4.437A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.345A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 239 through 244 removed outlier: 3.608A pdb=" N THR A 241 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.952A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.354A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 7.035A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.712A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 79 through 81 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.665A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 6.238A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.387A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.486A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.815A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.629A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 915 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.70 Time building geometry restraints manager: 11.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 11582 1.41 - 1.63: 16739 1.63 - 1.85: 274 1.85 - 2.07: 1 2.07 - 2.29: 80 Bond restraints: 28676 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.630 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.297 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" CB7 CDL N 202 " pdb=" OB8 CDL N 202 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+02 ... (remaining 28671 not shown) Histogram of bond angle deviations from ideal: 73.54 - 85.94: 76 85.94 - 98.33: 1 98.33 - 110.73: 9509 110.73 - 123.12: 27593 123.12 - 135.51: 1666 Bond angle restraints: 38845 Sorted by residual: angle pdb=" N GLY A 120 " pdb=" CA GLY A 120 " pdb=" C GLY A 120 " ideal model delta sigma weight residual 112.73 122.45 -9.72 1.20e+00 6.94e-01 6.57e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.06 -15.32 1.95e+00 2.62e-01 6.15e+01 angle pdb=" C ARG A 405 " pdb=" N PRO A 406 " pdb=" CA PRO A 406 " ideal model delta sigma weight residual 119.05 126.96 -7.91 1.11e+00 8.12e-01 5.07e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.15 -13.31 1.91e+00 2.73e-01 4.83e+01 angle pdb=" C TYR B 106 " pdb=" N PRO B 107 " pdb=" CA PRO B 107 " ideal model delta sigma weight residual 119.05 126.77 -7.72 1.11e+00 8.12e-01 4.83e+01 ... (remaining 38840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 16984 35.34 - 70.68: 366 70.68 - 106.01: 36 106.01 - 141.35: 4 141.35 - 176.69: 2 Dihedral angle restraints: 17392 sinusoidal: 7329 harmonic: 10063 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 74.28 -176.69 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -136.02 50.02 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA LEU I 106 " pdb=" C LEU I 106 " pdb=" N SER I 107 " pdb=" CA SER I 107 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 17389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3740 0.074 - 0.149: 445 0.149 - 0.223: 24 0.223 - 0.297: 7 0.297 - 0.372: 4 Chirality restraints: 4220 Sorted by residual: chirality pdb=" CA MET Q 222 " pdb=" N MET Q 222 " pdb=" C MET Q 222 " pdb=" CB MET Q 222 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ASN P 82 " pdb=" N ASN P 82 " pdb=" C ASN P 82 " pdb=" CB ASN P 82 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 4217 not shown) Planarity restraints: 4996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " -0.048 2.00e-02 2.50e+03 1.98e-01 4.91e+02 pdb=" C3N NDP J 401 " 0.387 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.111 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.169 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NDP J 401 " 0.115 2.00e-02 2.50e+03 2.05e-01 4.19e+02 pdb=" C2N NDP J 401 " 0.120 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.120 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.355 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP J 401 " -0.095 2.00e-02 2.50e+03 1.41e-01 2.00e+02 pdb=" C5N NDP J 401 " 0.175 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " -0.176 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " 0.095 2.00e-02 2.50e+03 ... (remaining 4993 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2009 2.73 - 3.27: 28143 3.27 - 3.82: 47077 3.82 - 4.36: 60872 4.36 - 4.90: 101264 Nonbonded interactions: 239365 Sorted by model distance: nonbonded pdb=" O GLU B 111 " pdb=" NH1 ARG B 141 " model vdw 2.190 2.520 nonbonded pdb=" NE2 GLN Q 149 " pdb=" OD2 ASP Q 309 " model vdw 2.209 2.520 nonbonded pdb=" OG1 THR M 487 " pdb=" OE1 GLN M 677 " model vdw 2.211 2.440 nonbonded pdb=" OD1 ASP B 165 " pdb=" NH2 ARG Q 368 " model vdw 2.212 2.520 nonbonded pdb=" OE1 GLU B 110 " pdb=" O CYS T 114 " model vdw 2.214 3.040 ... (remaining 239360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 7.400 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 79.430 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.008 0.312 28676 Z= 0.522 Angle : 0.803 16.430 38845 Z= 0.436 Chirality : 0.050 0.372 4220 Planarity : 0.007 0.205 4996 Dihedral : 15.158 176.690 10917 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.63 % Favored : 96.25 % Rotamer: Outliers : 0.23 % Allowed : 0.97 % Favored : 98.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.37 % 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: -0.02 (0.14), residues: 3439 helix: 0.68 (0.14), residues: 1320 sheet: 0.02 (0.26), residues: 390 loop : -0.49 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.027 0.002 PHE Q 204 TYR 0.041 0.002 TYR C 142 ARG 0.008 0.001 ARG K 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 631 time to evaluate : 3.297 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.6940 (ttpt) cc_final: 0.6715 (ttpt) REVERT: A 134 ASP cc_start: 0.8248 (p0) cc_final: 0.7984 (p0) REVERT: A 405 ARG cc_start: 0.7284 (mtm110) cc_final: 0.7005 (mtp180) REVERT: A 450 MET cc_start: 0.8961 (mtt) cc_final: 0.8581 (mtt) REVERT: B 208 ASP cc_start: 0.8050 (t70) cc_final: 0.7625 (t0) REVERT: C 49 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8440 (mmpt) REVERT: C 98 ARG cc_start: 0.6901 (ttp80) cc_final: 0.6686 (ttp-170) REVERT: C 126 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8230 (mt-10) REVERT: E 25 MET cc_start: 0.8345 (tpt) cc_final: 0.8039 (mmt) REVERT: E 30 ARG cc_start: 0.8193 (ttm110) cc_final: 0.7721 (mtm-85) REVERT: E 37 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7506 (mtt180) REVERT: F 35 ASP cc_start: 0.6797 (m-30) cc_final: 0.6585 (m-30) REVERT: G 114 ASP cc_start: 0.7515 (m-30) cc_final: 0.7176 (m-30) REVERT: I 62 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7969 (mt-10) REVERT: J 212 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7528 (mtm-85) REVERT: L 105 GLU cc_start: 0.8643 (tt0) cc_final: 0.8415 (tt0) REVERT: M 144 MET cc_start: 0.8736 (mmm) cc_final: 0.8426 (mmm) REVERT: N 21 ARG cc_start: 0.7137 (mmt180) cc_final: 0.6455 (mpt90) REVERT: Q 261 MET cc_start: 0.8843 (mmm) cc_final: 0.8624 (mmt) REVERT: Q 282 ASP cc_start: 0.8412 (m-30) cc_final: 0.8122 (m-30) REVERT: T 119 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7938 (ttp-170) outliers start: 7 outliers final: 6 residues processed: 637 average time/residue: 1.6425 time to fit residues: 1192.0458 Evaluate side-chains 439 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 433 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 83 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 0.2980 chunk 256 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 168 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN B 101 HIS E 48 HIS F 62 GLN F 86 GLN F 93 ASN G 142 GLN H 50 GLN I 9 GLN J 128 ASN J 166 HIS J 269 ASN J 278 GLN K 79 HIS K 110 HIS L 86 ASN M 74 ASN M 260 ASN M 336 ASN M 460 HIS M 499 ASN M 540 ASN M 604 GLN M 678 GLN N 31 ASN P 75 GLN P 77 GLN P 236 ASN Q 160 ASN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28676 Z= 0.316 Angle : 0.601 10.997 38845 Z= 0.310 Chirality : 0.046 0.216 4220 Planarity : 0.005 0.071 4996 Dihedral : 10.127 176.705 4071 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 2.20 % Allowed : 11.06 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.11 (0.14), residues: 3439 helix: 0.72 (0.14), residues: 1330 sheet: 0.16 (0.25), residues: 393 loop : -0.38 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 422 HIS 0.011 0.002 HIS Q 223 PHE 0.024 0.002 PHE Q 204 TYR 0.031 0.002 TYR C 142 ARG 0.008 0.001 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 451 time to evaluate : 3.523 Fit side-chains REVERT: A 102 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.6796 (tmm) REVERT: A 307 VAL cc_start: 0.8405 (p) cc_final: 0.8182 (t) REVERT: A 450 MET cc_start: 0.9024 (mtt) cc_final: 0.8623 (mtt) REVERT: B 208 ASP cc_start: 0.8018 (t70) cc_final: 0.7593 (t0) REVERT: C 126 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8231 (mt-10) REVERT: E 25 MET cc_start: 0.8444 (tpt) cc_final: 0.8094 (mmt) REVERT: E 52 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8559 (mt) REVERT: E 109 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: F 31 GLN cc_start: 0.8582 (tp40) cc_final: 0.7943 (tp40) REVERT: F 48 ASN cc_start: 0.8477 (m110) cc_final: 0.8191 (m110) REVERT: F 71 PHE cc_start: 0.7435 (m-10) cc_final: 0.7104 (m-80) REVERT: G 114 ASP cc_start: 0.7603 (m-30) cc_final: 0.7092 (m-30) REVERT: J 212 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7476 (mtm-85) REVERT: J 322 VAL cc_start: 0.8867 (p) cc_final: 0.8588 (m) REVERT: K 77 GLN cc_start: 0.8358 (mp10) cc_final: 0.7624 (mt0) REVERT: M 97 MET cc_start: 0.7611 (mmm) cc_final: 0.7350 (mmm) REVERT: M 144 MET cc_start: 0.8958 (mmm) cc_final: 0.8474 (mmm) REVERT: M 215 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6646 (mpt) REVERT: M 513 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8040 (mmm) REVERT: M 647 GLU cc_start: 0.7989 (tt0) cc_final: 0.7770 (tt0) REVERT: N 21 ARG cc_start: 0.7151 (mmt180) cc_final: 0.6459 (mpt90) REVERT: N 76 ASP cc_start: 0.7928 (m-30) cc_final: 0.7620 (m-30) REVERT: O 106 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: P 83 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: Q 81 THR cc_start: 0.8522 (m) cc_final: 0.8296 (t) outliers start: 66 outliers final: 23 residues processed: 479 average time/residue: 1.6197 time to fit residues: 886.2682 Evaluate side-chains 438 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 408 time to evaluate : 5.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 31 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 308 optimal weight: 0.0970 chunk 333 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 305 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 93 ASN I 9 GLN L 86 ASN M 460 HIS M 677 GLN ** N 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 135 GLN O 187 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28676 Z= 0.178 Angle : 0.510 10.641 38845 Z= 0.263 Chirality : 0.042 0.174 4220 Planarity : 0.004 0.061 4996 Dihedral : 9.639 178.113 4068 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 2.54 % Allowed : 12.66 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.31 (0.14), residues: 3439 helix: 0.98 (0.14), residues: 1322 sheet: 0.28 (0.26), residues: 387 loop : -0.35 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 422 HIS 0.008 0.001 HIS Q 223 PHE 0.016 0.001 PHE Q 84 TYR 0.021 0.001 TYR P 64 ARG 0.004 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 433 time to evaluate : 3.189 Fit side-chains REVERT: B 208 ASP cc_start: 0.7835 (t70) cc_final: 0.7451 (t0) REVERT: C 126 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8225 (mt-10) REVERT: E 52 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8606 (mt) REVERT: E 109 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: F 31 GLN cc_start: 0.8543 (tp40) cc_final: 0.8277 (tp40) REVERT: F 71 PHE cc_start: 0.7303 (m-10) cc_final: 0.6962 (m-10) REVERT: F 91 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8570 (tt) REVERT: G 80 LYS cc_start: 0.8297 (tttt) cc_final: 0.8080 (ttpp) REVERT: G 114 ASP cc_start: 0.7604 (m-30) cc_final: 0.7078 (m-30) REVERT: H 70 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: J 212 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7559 (mtm-85) REVERT: K 75 ASN cc_start: 0.8459 (t160) cc_final: 0.8011 (t0) REVERT: M 97 MET cc_start: 0.7671 (mmm) cc_final: 0.7379 (mmm) REVERT: M 144 MET cc_start: 0.8948 (mmm) cc_final: 0.8368 (mmm) REVERT: M 215 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6713 (mpt) REVERT: M 535 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6538 (mp0) REVERT: N 21 ARG cc_start: 0.7162 (mmt180) cc_final: 0.6470 (mpt90) REVERT: N 76 ASP cc_start: 0.7954 (m-30) cc_final: 0.7612 (m-30) REVERT: N 142 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.7176 (p) REVERT: O 106 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7989 (mp10) REVERT: P 50 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6899 (ttt90) REVERT: P 63 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8183 (mm110) REVERT: P 83 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: T 119 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.8025 (ttm170) outliers start: 76 outliers final: 25 residues processed: 467 average time/residue: 1.5896 time to fit residues: 849.4870 Evaluate side-chains 448 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 413 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 396 GLU Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 4.9990 chunk 231 optimal weight: 0.0770 chunk 160 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 327 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN F 62 GLN F 93 ASN I 9 GLN L 86 ASN M 74 ASN M 460 HIS M 677 GLN M 678 GLN N 13 GLN N 31 ASN N 135 GLN O 189 ASN T 63 ASN W 24 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28676 Z= 0.292 Angle : 0.563 10.783 38845 Z= 0.291 Chirality : 0.045 0.186 4220 Planarity : 0.005 0.065 4996 Dihedral : 9.497 177.926 4067 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 3.01 % Allowed : 13.83 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.23 (0.14), residues: 3439 helix: 0.89 (0.14), residues: 1334 sheet: 0.13 (0.26), residues: 389 loop : -0.36 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.010 0.001 HIS J 37 PHE 0.020 0.002 PHE Q 204 TYR 0.021 0.002 TYR P 64 ARG 0.007 0.001 ARG M 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 424 time to evaluate : 3.075 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8970 (tt) REVERT: B 208 ASP cc_start: 0.7876 (t70) cc_final: 0.7482 (t0) REVERT: C 126 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8240 (mt-10) REVERT: E 66 MET cc_start: 0.8632 (mmp) cc_final: 0.8201 (mmp) REVERT: E 109 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: F 71 PHE cc_start: 0.7733 (m-10) cc_final: 0.7480 (m-10) REVERT: G 82 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6874 (mtp180) REVERT: G 114 ASP cc_start: 0.7663 (m-30) cc_final: 0.7201 (m-30) REVERT: G 134 ASP cc_start: 0.8272 (p0) cc_final: 0.7963 (p0) REVERT: I 70 MET cc_start: 0.8515 (tmt) cc_final: 0.8204 (tmt) REVERT: J 212 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7536 (mtm-85) REVERT: J 322 VAL cc_start: 0.9080 (p) cc_final: 0.8722 (t) REVERT: M 144 MET cc_start: 0.8968 (mmm) cc_final: 0.8379 (mmm) REVERT: M 158 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8656 (ptt180) REVERT: M 173 MET cc_start: 0.9088 (mmm) cc_final: 0.8816 (mmm) REVERT: M 215 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7021 (mpt) REVERT: M 535 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6637 (mp0) REVERT: N 21 ARG cc_start: 0.7197 (mmt180) cc_final: 0.6476 (mpt90) REVERT: N 76 ASP cc_start: 0.7969 (m-30) cc_final: 0.7644 (m-30) REVERT: N 142 THR cc_start: 0.7421 (OUTLIER) cc_final: 0.7166 (p) REVERT: O 106 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: O 134 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9039 (t) REVERT: P 50 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6923 (ttt90) REVERT: P 63 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8273 (mm110) REVERT: P 83 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: T 119 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.8034 (ttm170) outliers start: 90 outliers final: 40 residues processed: 466 average time/residue: 1.6130 time to fit residues: 861.7534 Evaluate side-chains 451 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 400 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 396 GLU Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 4 optimal weight: 0.0030 chunk 243 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 294 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN F 62 GLN F 93 ASN I 9 GLN L 86 ASN N 31 ASN N 135 GLN O 187 GLN W 24 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28676 Z= 0.208 Angle : 0.518 10.672 38845 Z= 0.267 Chirality : 0.043 0.178 4220 Planarity : 0.004 0.062 4996 Dihedral : 9.162 178.609 4067 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 2.77 % Allowed : 15.13 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.30 (0.14), residues: 3439 helix: 1.01 (0.14), residues: 1322 sheet: 0.08 (0.25), residues: 401 loop : -0.33 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.008 0.001 HIS J 37 PHE 0.013 0.001 PHE Q 204 TYR 0.018 0.001 TYR P 64 ARG 0.006 0.000 ARG M 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 418 time to evaluate : 4.062 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8940 (tt) REVERT: B 208 ASP cc_start: 0.7844 (t70) cc_final: 0.7466 (t0) REVERT: C 65 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7657 (tmm) REVERT: C 126 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8262 (mt-10) REVERT: E 66 MET cc_start: 0.8675 (mmp) cc_final: 0.8241 (mmp) REVERT: F 71 PHE cc_start: 0.7696 (m-10) cc_final: 0.7474 (m-10) REVERT: G 80 LYS cc_start: 0.8226 (tttt) cc_final: 0.7985 (ttpp) REVERT: G 82 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6791 (mtp180) REVERT: G 114 ASP cc_start: 0.7661 (m-30) cc_final: 0.7275 (m-30) REVERT: G 134 ASP cc_start: 0.8118 (p0) cc_final: 0.7840 (p0) REVERT: H 70 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: I 70 MET cc_start: 0.8415 (tmt) cc_final: 0.8133 (tmt) REVERT: J 212 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7596 (mtm-85) REVERT: J 322 VAL cc_start: 0.9108 (p) cc_final: 0.8790 (t) REVERT: K 75 ASN cc_start: 0.8456 (t160) cc_final: 0.8045 (t0) REVERT: L 105 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: M 144 MET cc_start: 0.8816 (mmm) cc_final: 0.8270 (mmm) REVERT: M 173 MET cc_start: 0.9107 (mmm) cc_final: 0.8827 (mmm) REVERT: M 215 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7053 (mpt) REVERT: M 535 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6637 (mp0) REVERT: N 21 ARG cc_start: 0.7218 (mmt180) cc_final: 0.6484 (mpt90) REVERT: N 25 ARG cc_start: 0.7908 (ttt90) cc_final: 0.7659 (ttt180) REVERT: N 76 ASP cc_start: 0.7931 (m-30) cc_final: 0.7629 (m-30) REVERT: O 106 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: O 168 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8166 (mp) REVERT: P 50 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6899 (ttt90) REVERT: T 119 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.7888 (ttm170) outliers start: 83 outliers final: 38 residues processed: 459 average time/residue: 1.5923 time to fit residues: 837.2949 Evaluate side-chains 449 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 402 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 396 GLU Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 327 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN F 62 GLN F 93 ASN G 115 GLN I 9 GLN L 86 ASN N 135 GLN W 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28676 Z= 0.344 Angle : 0.586 10.862 38845 Z= 0.302 Chirality : 0.046 0.189 4220 Planarity : 0.005 0.065 4996 Dihedral : 9.213 178.189 4064 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 2.74 % Allowed : 15.63 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.10 (0.14), residues: 3439 helix: 0.78 (0.14), residues: 1336 sheet: -0.00 (0.25), residues: 400 loop : -0.41 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.011 0.001 HIS J 37 PHE 0.018 0.002 PHE Q 204 TYR 0.019 0.002 TYR P 64 ARG 0.006 0.001 ARG M 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 404 time to evaluate : 3.385 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.9000 (tt) REVERT: B 208 ASP cc_start: 0.7937 (t70) cc_final: 0.7542 (t0) REVERT: C 65 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7660 (tmm) REVERT: C 126 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8292 (mt-10) REVERT: E 109 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: G 114 ASP cc_start: 0.7724 (m-30) cc_final: 0.7373 (m-30) REVERT: G 134 ASP cc_start: 0.8058 (p0) cc_final: 0.7780 (p0) REVERT: I 70 MET cc_start: 0.8471 (tmt) cc_final: 0.8200 (tmt) REVERT: J 212 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7721 (mpp-170) REVERT: J 322 VAL cc_start: 0.9168 (p) cc_final: 0.8939 (t) REVERT: M 173 MET cc_start: 0.9135 (mmm) cc_final: 0.8853 (mmm) REVERT: M 215 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7077 (mpt) REVERT: M 535 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6730 (mp0) REVERT: M 643 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7678 (mtt180) REVERT: N 21 ARG cc_start: 0.7129 (mmt180) cc_final: 0.6489 (mtt90) REVERT: N 76 ASP cc_start: 0.8065 (m-30) cc_final: 0.7726 (m-30) REVERT: N 142 THR cc_start: 0.7365 (OUTLIER) cc_final: 0.7113 (p) REVERT: O 106 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: O 168 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8221 (mp) REVERT: Q 96 ARG cc_start: 0.8273 (ttt180) cc_final: 0.8002 (ttt-90) REVERT: T 119 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7896 (ttm170) outliers start: 82 outliers final: 44 residues processed: 447 average time/residue: 1.5951 time to fit residues: 819.2066 Evaluate side-chains 448 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 396 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 396 GLU Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 239 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 276 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN F 62 GLN F 93 ASN G 115 GLN I 9 GLN ** K 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 652 ASN N 31 ASN N 135 GLN W 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28676 Z= 0.199 Angle : 0.517 10.639 38845 Z= 0.267 Chirality : 0.042 0.175 4220 Planarity : 0.004 0.063 4996 Dihedral : 8.942 179.069 4064 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.40 % Allowed : 16.23 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.24 (0.14), residues: 3439 helix: 0.94 (0.14), residues: 1332 sheet: 0.01 (0.25), residues: 404 loop : -0.35 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.013 0.001 PHE A 101 TYR 0.016 0.001 TYR P 64 ARG 0.006 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 413 time to evaluate : 3.264 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7642 (tp) REVERT: B 208 ASP cc_start: 0.7864 (t70) cc_final: 0.7453 (t0) REVERT: C 65 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7651 (tmm) REVERT: C 126 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8261 (mt-10) REVERT: E 109 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: G 80 LYS cc_start: 0.8232 (tttt) cc_final: 0.8001 (ttpp) REVERT: G 114 ASP cc_start: 0.7672 (m-30) cc_final: 0.7327 (m-30) REVERT: G 134 ASP cc_start: 0.7966 (p0) cc_final: 0.7724 (p0) REVERT: I 70 MET cc_start: 0.8334 (tmt) cc_final: 0.8074 (tmt) REVERT: J 212 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7631 (mtm-85) REVERT: J 316 ARG cc_start: 0.6406 (mpt180) cc_final: 0.5500 (mmt180) REVERT: J 322 VAL cc_start: 0.9152 (p) cc_final: 0.8915 (t) REVERT: K 75 ASN cc_start: 0.8442 (t160) cc_final: 0.7973 (t0) REVERT: L 105 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: M 173 MET cc_start: 0.9137 (mmm) cc_final: 0.8858 (mmm) REVERT: M 215 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7004 (mpt) REVERT: M 643 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.7638 (mtt180) REVERT: N 21 ARG cc_start: 0.7172 (mmt180) cc_final: 0.6469 (mtt90) REVERT: N 76 ASP cc_start: 0.7996 (m-30) cc_final: 0.7665 (m-30) REVERT: O 106 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: O 168 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8269 (mp) REVERT: P 240 GLU cc_start: 0.8171 (pt0) cc_final: 0.7970 (pp20) REVERT: T 119 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.7935 (ttm170) outliers start: 72 outliers final: 35 residues processed: 449 average time/residue: 1.6459 time to fit residues: 845.6024 Evaluate side-chains 445 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 402 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 222 optimal weight: 0.3980 chunk 161 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN C 123 GLN F 62 GLN I 9 GLN ** K 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 678 GLN N 31 ASN N 135 GLN O 187 GLN Q 147 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28676 Z= 0.178 Angle : 0.510 10.541 38845 Z= 0.261 Chirality : 0.042 0.178 4220 Planarity : 0.004 0.059 4996 Dihedral : 8.774 179.157 4062 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 2.27 % Allowed : 16.60 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.35 (0.14), residues: 3439 helix: 1.03 (0.14), residues: 1333 sheet: 0.05 (0.25), residues: 394 loop : -0.29 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.012 0.001 PHE A 101 TYR 0.016 0.001 TYR P 64 ARG 0.008 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 414 time to evaluate : 4.240 Fit side-chains REVERT: A 97 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7626 (tp) REVERT: B 208 ASP cc_start: 0.7840 (t70) cc_final: 0.7443 (t0) REVERT: C 65 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7636 (tmm) REVERT: C 99 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: C 126 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8258 (mt-10) REVERT: E 109 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: G 114 ASP cc_start: 0.7647 (m-30) cc_final: 0.7331 (m-30) REVERT: G 134 ASP cc_start: 0.7978 (p0) cc_final: 0.7715 (p0) REVERT: I 109 ASP cc_start: 0.8257 (t0) cc_final: 0.8043 (OUTLIER) REVERT: J 212 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7635 (mtm-85) REVERT: J 316 ARG cc_start: 0.6316 (mpt180) cc_final: 0.5455 (mmt180) REVERT: J 322 VAL cc_start: 0.9153 (p) cc_final: 0.8924 (t) REVERT: K 75 ASN cc_start: 0.8442 (t160) cc_final: 0.7973 (t0) REVERT: L 105 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: M 77 MET cc_start: 0.8492 (tpt) cc_final: 0.8178 (tpt) REVERT: M 173 MET cc_start: 0.9130 (mmm) cc_final: 0.8930 (mmm) REVERT: M 215 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7020 (mpt) REVERT: M 643 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7586 (mtt180) REVERT: N 21 ARG cc_start: 0.7173 (mmt180) cc_final: 0.6486 (mtt90) REVERT: N 67 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: N 76 ASP cc_start: 0.7948 (m-30) cc_final: 0.7637 (m-30) REVERT: O 106 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: O 168 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8274 (mp) REVERT: T 119 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7867 (ttm170) outliers start: 68 outliers final: 38 residues processed: 453 average time/residue: 1.6154 time to fit residues: 838.4963 Evaluate side-chains 449 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 402 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 5.9990 chunk 313 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 275 optimal weight: 0.6980 chunk 287 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN E 45 ASN F 62 GLN I 9 GLN L 86 ASN N 31 ASN N 135 GLN O 187 GLN Q 147 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28676 Z= 0.258 Angle : 0.544 10.771 38845 Z= 0.280 Chirality : 0.044 0.188 4220 Planarity : 0.005 0.062 4996 Dihedral : 8.824 177.836 4062 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.30 % Allowed : 16.97 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.29 (0.14), residues: 3439 helix: 0.97 (0.14), residues: 1332 sheet: 0.08 (0.25), residues: 402 loop : -0.33 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.009 0.001 HIS J 37 PHE 0.016 0.001 PHE A 101 TYR 0.016 0.001 TYR P 64 ARG 0.009 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 404 time to evaluate : 3.437 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7637 (tp) REVERT: B 208 ASP cc_start: 0.7877 (t70) cc_final: 0.7459 (t0) REVERT: C 65 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7649 (tmm) REVERT: C 99 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7079 (pt0) REVERT: C 126 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8268 (mt-10) REVERT: C 195 ARG cc_start: 0.7848 (mtt-85) cc_final: 0.7629 (mtt90) REVERT: E 23 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7090 (mtp-110) REVERT: E 109 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: G 114 ASP cc_start: 0.7762 (m-30) cc_final: 0.7409 (m-30) REVERT: G 134 ASP cc_start: 0.7985 (p0) cc_final: 0.7766 (p0) REVERT: I 109 ASP cc_start: 0.8164 (t0) cc_final: 0.7950 (OUTLIER) REVERT: J 212 ARG cc_start: 0.7928 (mtt180) cc_final: 0.7636 (mtm-85) REVERT: J 316 ARG cc_start: 0.6310 (mpt180) cc_final: 0.5443 (mmt180) REVERT: J 322 VAL cc_start: 0.9162 (p) cc_final: 0.8918 (t) REVERT: K 75 ASN cc_start: 0.8447 (t160) cc_final: 0.7969 (t0) REVERT: M 77 MET cc_start: 0.8700 (tpt) cc_final: 0.8444 (tpt) REVERT: M 215 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7024 (mpt) REVERT: M 643 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7594 (mtt180) REVERT: N 21 ARG cc_start: 0.7202 (mmt180) cc_final: 0.6491 (mtt90) REVERT: N 41 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: N 67 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: N 76 ASP cc_start: 0.8003 (m-30) cc_final: 0.7661 (m-30) REVERT: O 106 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: O 168 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8256 (mp) REVERT: T 119 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7840 (ttm170) outliers start: 69 outliers final: 45 residues processed: 442 average time/residue: 1.6167 time to fit residues: 821.0216 Evaluate side-chains 461 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 406 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 396 GLU Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 321 optimal weight: 0.2980 chunk 196 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 223 optimal weight: 0.8980 chunk 337 optimal weight: 0.0670 chunk 310 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN E 45 ASN F 62 GLN I 9 GLN L 86 ASN M 678 GLN N 31 ASN N 135 GLN O 187 GLN Q 147 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28676 Z= 0.156 Angle : 0.504 12.545 38845 Z= 0.257 Chirality : 0.041 0.175 4220 Planarity : 0.004 0.060 4996 Dihedral : 8.588 178.873 4062 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 1.67 % Allowed : 17.64 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3439 helix: 1.12 (0.15), residues: 1330 sheet: 0.12 (0.25), residues: 392 loop : -0.24 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.016 0.001 PHE A 101 TYR 0.014 0.001 TYR P 64 ARG 0.010 0.000 ARG C 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 417 time to evaluate : 3.706 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7630 (tp) REVERT: B 208 ASP cc_start: 0.7836 (t70) cc_final: 0.7438 (t0) REVERT: C 99 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7045 (pt0) REVERT: C 126 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8236 (mt-10) REVERT: E 23 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7088 (mtp-110) REVERT: E 109 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: G 114 ASP cc_start: 0.7695 (m-30) cc_final: 0.7397 (m-30) REVERT: G 134 ASP cc_start: 0.7908 (p0) cc_final: 0.7700 (p0) REVERT: I 109 ASP cc_start: 0.8156 (t0) cc_final: 0.7955 (t0) REVERT: J 212 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7641 (mtm-85) REVERT: J 316 ARG cc_start: 0.6230 (mpt180) cc_final: 0.5453 (mmt180) REVERT: J 319 VAL cc_start: 0.8764 (m) cc_final: 0.8521 (t) REVERT: J 322 VAL cc_start: 0.9166 (p) cc_final: 0.8927 (t) REVERT: K 75 ASN cc_start: 0.8421 (t160) cc_final: 0.7950 (t0) REVERT: M 77 MET cc_start: 0.8571 (tpt) cc_final: 0.8215 (tpt) REVERT: M 215 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6686 (mpt) REVERT: M 535 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6537 (mp0) REVERT: N 21 ARG cc_start: 0.7182 (mmt180) cc_final: 0.6490 (mtt90) REVERT: N 41 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: N 76 ASP cc_start: 0.7968 (m-30) cc_final: 0.7657 (m-30) REVERT: O 106 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: O 168 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8292 (mp) REVERT: P 50 ARG cc_start: 0.7069 (ttt90) cc_final: 0.6833 (ttt90) REVERT: T 119 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7822 (ttm170) outliers start: 50 outliers final: 30 residues processed: 444 average time/residue: 1.6315 time to fit residues: 828.6812 Evaluate side-chains 441 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 403 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN E 45 ASN H 73 GLN I 9 GLN J 376 ASN L 86 ASN M 678 GLN N 31 ASN N 135 GLN O 187 GLN Q 147 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.086920 restraints weight = 37133.439| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.35 r_work: 0.2777 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28676 Z= 0.292 Angle : 0.563 12.162 38845 Z= 0.290 Chirality : 0.044 0.186 4220 Planarity : 0.005 0.062 4996 Dihedral : 8.778 176.332 4062 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 1.84 % Allowed : 17.70 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.29 (0.14), residues: 3439 helix: 0.95 (0.14), residues: 1337 sheet: 0.11 (0.25), residues: 396 loop : -0.31 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 422 HIS 0.010 0.001 HIS J 37 PHE 0.016 0.002 PHE Q 84 TYR 0.016 0.002 TYR P 64 ARG 0.007 0.000 ARG B 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12196.17 seconds wall clock time: 216 minutes 34.38 seconds (12994.38 seconds total)