Starting phenix.real_space_refine on Fri Feb 23 03:49:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybp_10770/02_2024/6ybp_10770_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybp_10770/02_2024/6ybp_10770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybp_10770/02_2024/6ybp_10770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybp_10770/02_2024/6ybp_10770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybp_10770/02_2024/6ybp_10770_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybp_10770/02_2024/6ybp_10770_updated.pdb" } resolution = 3.48 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= 0.008 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 157 5.16 5 C 22970 2.51 5 N 6423 2.21 5 O 6842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B ARG 288": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D GLU 499": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 119": "NH1" <-> "NH2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "E ARG 288": "NH1" <-> "NH2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E ARG 399": "NH1" <-> "NH2" Residue "E ARG 453": "NH1" <-> "NH2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 185": "NH1" <-> "NH2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F ARG 288": "NH1" <-> "NH2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F ARG 305": "NH1" <-> "NH2" Residue "F ARG 399": "NH1" <-> "NH2" Residue "F ARG 453": "NH1" <-> "NH2" Residue "F GLU 458": "OE1" <-> "OE2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "G GLU 336": "OE1" <-> "OE2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G GLU 403": "OE1" <-> "OE2" Residue "G ARG 421": "NH1" <-> "NH2" Residue "G ARG 435": "NH1" <-> "NH2" Residue "G GLU 460": "OE1" <-> "OE2" Residue "G ARG 483": "NH1" <-> "NH2" Residue "G ARG 499": "NH1" <-> "NH2" Residue "G ARG 501": "NH1" <-> "NH2" Residue "G ARG 509": "NH1" <-> "NH2" Residue "G ARG 534": "NH1" <-> "NH2" Residue "G ARG 538": "NH1" <-> "NH2" Residue "G ARG 558": "NH1" <-> "NH2" Residue "G ARG 576": "NH1" <-> "NH2" Residue "G ARG 580": "NH1" <-> "NH2" Residue "G GLU 584": "OE1" <-> "OE2" Residue "G ARG 642": "NH1" <-> "NH2" Residue "G GLU 653": "OE1" <-> "OE2" Residue "H ARG 483": "NH1" <-> "NH2" Residue "H ARG 499": "NH1" <-> "NH2" Residue "H GLU 500": "OE1" <-> "OE2" Residue "H ARG 501": "NH1" <-> "NH2" Residue "H ARG 509": "NH1" <-> "NH2" Residue "H ARG 534": "NH1" <-> "NH2" Residue "H ARG 538": "NH1" <-> "NH2" Residue "H ARG 558": "NH1" <-> "NH2" Residue "H ARG 576": "NH1" <-> "NH2" Residue "H ARG 580": "NH1" <-> "NH2" Residue "H GLU 584": "OE1" <-> "OE2" Residue "H GLU 593": "OE1" <-> "OE2" Residue "H GLU 616": "OE1" <-> "OE2" Residue "H GLU 635": "OE1" <-> "OE2" Residue "H ARG 642": "NH1" <-> "NH2" Residue "H GLU 665": "OE1" <-> "OE2" Residue "I GLU 342": "OE1" <-> "OE2" Residue "I ARG 354": "NH1" <-> "NH2" Residue "I ARG 372": "NH1" <-> "NH2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I GLU 403": "OE1" <-> "OE2" Residue "I GLU 406": "OE1" <-> "OE2" Residue "I GLU 418": "OE1" <-> "OE2" Residue "I ARG 421": "NH1" <-> "NH2" Residue "I ARG 483": "NH1" <-> "NH2" Residue "I ARG 499": "NH1" <-> "NH2" Residue "I GLU 500": "OE1" <-> "OE2" Residue "I ARG 501": "NH1" <-> "NH2" Residue "I ARG 509": "NH1" <-> "NH2" Residue "I ARG 534": "NH1" <-> "NH2" Residue "I ARG 538": "NH1" <-> "NH2" Residue "I ARG 558": "NH1" <-> "NH2" Residue "I ARG 576": "NH1" <-> "NH2" Residue "I ARG 580": "NH1" <-> "NH2" Residue "I GLU 584": "OE1" <-> "OE2" Residue "I ARG 642": "NH1" <-> "NH2" Residue "I GLU 665": "OE1" <-> "OE2" Residue "J GLU 382": "OE1" <-> "OE2" Residue "J ARG 401": "NH1" <-> "NH2" Residue "J GLU 403": "OE1" <-> "OE2" Residue "J ARG 421": "NH1" <-> "NH2" Residue "J GLU 460": "OE1" <-> "OE2" Residue "J ARG 483": "NH1" <-> "NH2" Residue "J ARG 499": "NH1" <-> "NH2" Residue "J ARG 501": "NH1" <-> "NH2" Residue "J ARG 509": "NH1" <-> "NH2" Residue "J ARG 534": "NH1" <-> "NH2" Residue "J ARG 538": "NH1" <-> "NH2" Residue "J ARG 558": "NH1" <-> "NH2" Residue "J ARG 576": "NH1" <-> "NH2" Residue "J ARG 580": "NH1" <-> "NH2" Residue "J GLU 582": "OE1" <-> "OE2" Residue "J GLU 635": "OE1" <-> "OE2" Residue "J GLU 641": "OE1" <-> "OE2" Residue "J ARG 642": "NH1" <-> "NH2" Residue "J GLU 665": "OE1" <-> "OE2" Residue "K GLU 336": "OE1" <-> "OE2" Residue "K GLU 342": "OE1" <-> "OE2" Residue "K GLU 418": "OE1" <-> "OE2" Residue "K ARG 435": "NH1" <-> "NH2" Residue "K ARG 483": "NH1" <-> "NH2" Residue "K ARG 499": "NH1" <-> "NH2" Residue "K GLU 500": "OE1" <-> "OE2" Residue "K ARG 501": "NH1" <-> "NH2" Residue "K ARG 509": "NH1" <-> "NH2" Residue "K ARG 534": "NH1" <-> "NH2" Residue "K ARG 538": "NH1" <-> "NH2" Residue "K ARG 558": "NH1" <-> "NH2" Residue "K ARG 576": "NH1" <-> "NH2" Residue "K ARG 580": "NH1" <-> "NH2" Residue "K GLU 582": "OE1" <-> "OE2" Residue "K GLU 584": "OE1" <-> "OE2" Residue "K ARG 642": "NH1" <-> "NH2" Residue "K GLU 653": "OE1" <-> "OE2" Residue "L GLU 382": "OE1" <-> "OE2" Residue "L GLU 418": "OE1" <-> "OE2" Residue "L ARG 421": "NH1" <-> "NH2" Residue "L ARG 435": "NH1" <-> "NH2" Residue "L ARG 466": "NH1" <-> "NH2" Residue "L ARG 483": "NH1" <-> "NH2" Residue "L ARG 499": "NH1" <-> "NH2" Residue "L ARG 501": "NH1" <-> "NH2" Residue "L ARG 509": "NH1" <-> "NH2" Residue "L ARG 534": "NH1" <-> "NH2" Residue "L ARG 538": "NH1" <-> "NH2" Residue "L ARG 558": "NH1" <-> "NH2" Residue "L ARG 576": "NH1" <-> "NH2" Residue "L ARG 580": "NH1" <-> "NH2" Residue "L GLU 619": "OE1" <-> "OE2" Residue "L ARG 642": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36410 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "B" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "C" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "D" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "E" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "F" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "G" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2135 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 18, 'TRANS': 264} Chain breaks: 5 Chain: "H" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1565 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "I" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2183 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 17, 'TRANS': 270} Chain breaks: 4 Chain: "J" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2305 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 20, 'TRANS': 282} Chain breaks: 3 Chain: "K" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2217 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 18, 'TRANS': 274} Chain breaks: 4 Chain: "L" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2208 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 18, 'TRANS': 272} Chain breaks: 4 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'COA:plan-3': 1, 'COA:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'COA:plan-3': 1, 'COA:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'COA:plan-3': 1, 'COA:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.29, per 1000 atoms: 0.50 Number of scatterers: 36410 At special positions: 0 Unit cell: (160.48, 160.48, 175.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 157 16.00 P 18 15.00 O 6842 8.00 N 6423 7.00 C 22970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.46 Conformation dependent library (CDL) restraints added in 6.7 seconds 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8554 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 45 sheets defined 34.6% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.40 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 removed outlier: 3.674A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.597A pdb=" N ARG A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 133 through 153 removed outlier: 6.912A pdb=" N VAL A 137 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 138 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.868A pdb=" N ASP A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.950A pdb=" N LEU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 479 through 495 removed outlier: 5.084A pdb=" N ARG A 483 " --> pdb=" O HIS A 480 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 490 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR A 495 " --> pdb=" O MET A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 17 removed outlier: 3.980A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 133 through 153 removed outlier: 6.768A pdb=" N VAL B 137 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 138 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.874A pdb=" N ASP B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 375 through 388 removed outlier: 3.945A pdb=" N LEU B 382 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 479 through 495 removed outlier: 5.149A pdb=" N ARG B 483 " --> pdb=" O HIS B 480 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 490 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 494 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR B 495 " --> pdb=" O MET B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 17 removed outlier: 3.970A pdb=" N LEU C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 35 through 42 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 102 through 118 Processing helix chain 'C' and resid 133 through 153 removed outlier: 6.886A pdb=" N VAL C 137 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 138 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 231 through 243 removed outlier: 3.906A pdb=" N ASP C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 271 Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 388 removed outlier: 3.896A pdb=" N LEU C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 441 through 443 No H-bonds generated for 'chain 'C' and resid 441 through 443' Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 479 through 495 removed outlier: 5.252A pdb=" N ARG C 483 " --> pdb=" O HIS C 480 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 490 " --> pdb=" O ALA C 487 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR C 495 " --> pdb=" O MET C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 35 through 42 Processing helix chain 'D' and resid 61 through 66 removed outlier: 5.819A pdb=" N GLU D 65 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 102 through 118 removed outlier: 3.730A pdb=" N LYS D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 108 " --> pdb=" O HIS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 153 removed outlier: 6.737A pdb=" N VAL D 137 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 138 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 176 Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.999A pdb=" N ASP D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 375 through 388 removed outlier: 3.945A pdb=" N LEU D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 383 " --> pdb=" O GLY D 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 388 " --> pdb=" O PHE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.612A pdb=" N ARG D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 495 removed outlier: 5.147A pdb=" N ARG D 483 " --> pdb=" O HIS D 480 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU D 490 " --> pdb=" O ALA D 487 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG D 494 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR D 495 " --> pdb=" O MET D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 17 removed outlier: 3.684A pdb=" N LEU E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 29 Processing helix chain 'E' and resid 35 through 42 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 102 through 118 removed outlier: 3.732A pdb=" N LYS E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 108 " --> pdb=" O HIS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 153 removed outlier: 6.718A pdb=" N VAL E 137 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA E 138 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 176 Proline residue: E 175 - end of helix Processing helix chain 'E' and resid 195 through 202 Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 231 through 244 removed outlier: 3.695A pdb=" N ASP E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 271 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 375 through 388 removed outlier: 4.103A pdb=" N LEU E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 383 " --> pdb=" O GLY E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 432 through 439 Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 448 through 461 Processing helix chain 'E' and resid 465 through 469 Processing helix chain 'E' and resid 479 through 495 removed outlier: 5.408A pdb=" N ARG E 483 " --> pdb=" O HIS E 480 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU E 490 " --> pdb=" O ALA E 487 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG E 494 " --> pdb=" O GLY E 491 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR E 495 " --> pdb=" O MET E 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 17 removed outlier: 4.073A pdb=" N LEU F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 29 Processing helix chain 'F' and resid 35 through 42 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 102 through 118 Processing helix chain 'F' and resid 133 through 153 removed outlier: 6.557A pdb=" N VAL F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 Proline residue: F 175 - end of helix Processing helix chain 'F' and resid 195 through 202 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 231 through 244 removed outlier: 3.849A pdb=" N ASP F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 271 Processing helix chain 'F' and resid 283 through 290 Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 375 through 388 removed outlier: 4.036A pdb=" N LEU F 382 " --> pdb=" O HIS F 378 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 383 " --> pdb=" O GLY F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 408 Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 432 through 439 Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 448 through 461 Processing helix chain 'F' and resid 465 through 469 Processing helix chain 'F' and resid 479 through 495 removed outlier: 5.214A pdb=" N ARG F 483 " --> pdb=" O HIS F 480 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU F 490 " --> pdb=" O ALA F 487 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR F 495 " --> pdb=" O MET F 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 411 Processing helix chain 'G' and resid 425 through 429 Processing helix chain 'G' and resid 461 through 484 removed outlier: 4.701A pdb=" N GLY G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 588 removed outlier: 4.311A pdb=" N LEU G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 484 removed outlier: 3.873A pdb=" N GLY H 484 " --> pdb=" O ILE H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 580 through 588 removed outlier: 3.895A pdb=" N LEU H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 413 Processing helix chain 'I' and resid 424 through 429 Processing helix chain 'I' and resid 461 through 484 removed outlier: 3.773A pdb=" N ARG I 466 " --> pdb=" O PRO I 462 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY I 484 " --> pdb=" O ILE I 480 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 494 No H-bonds generated for 'chain 'I' and resid 492 through 494' Processing helix chain 'I' and resid 580 through 588 removed outlier: 3.620A pdb=" N ASP I 587 " --> pdb=" O ALA I 583 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 402 through 414 Processing helix chain 'J' and resid 424 through 432 Processing helix chain 'J' and resid 461 through 482 Processing helix chain 'J' and resid 580 through 585 Processing helix chain 'K' and resid 401 through 414 Processing helix chain 'K' and resid 424 through 432 Processing helix chain 'K' and resid 461 through 484 removed outlier: 4.184A pdb=" N HIS K 465 " --> pdb=" O GLY K 461 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG K 466 " --> pdb=" O PRO K 462 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL K 470 " --> pdb=" O ARG K 466 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP K 475 " --> pdb=" O ALA K 471 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY K 484 " --> pdb=" O ILE K 480 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 494 No H-bonds generated for 'chain 'K' and resid 492 through 494' Processing helix chain 'K' and resid 580 through 588 removed outlier: 3.812A pdb=" N ASP K 587 " --> pdb=" O ALA K 583 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU K 588 " --> pdb=" O GLU K 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 412 Processing helix chain 'L' and resid 424 through 431 Processing helix chain 'L' and resid 461 through 484 removed outlier: 4.759A pdb=" N GLY L 484 " --> pdb=" O ILE L 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 494 No H-bonds generated for 'chain 'L' and resid 492 through 494' Processing helix chain 'L' and resid 580 through 587 Processing sheet with id= A, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.811A pdb=" N THR A 76 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE A 89 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 123 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N LYS A 91 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE A 125 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE A 180 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE A 163 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 182 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 166 through 168 removed outlier: 6.194A pdb=" N TYR A 189 " --> pdb=" O CYS A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 307 through 314 removed outlier: 6.657A pdb=" N LEU A 418 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE A 397 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR A 420 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.301A pdb=" N GLN A 426 " --> pdb=" O ALA A 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 74 through 81 removed outlier: 8.212A pdb=" N PHE B 89 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE B 123 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LYS B 91 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 125 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE B 180 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE B 163 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE B 182 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B 226 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.188A pdb=" N TYR B 189 " --> pdb=" O CYS B 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 307 through 314 removed outlier: 5.557A pdb=" N ASP B 360 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL B 361 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS B 400 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 418 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE B 397 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR B 420 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG B 399 " --> pdb=" O TYR B 420 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 74 through 81 removed outlier: 8.411A pdb=" N PHE C 89 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 123 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LYS C 91 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE C 125 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE C 180 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE C 163 " --> pdb=" O PHE C 180 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE C 182 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY C 226 " --> pdb=" O MET C 183 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 307 through 314 removed outlier: 6.417A pdb=" N LEU C 418 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE C 397 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR C 420 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 400 through 402 removed outlier: 6.528A pdb=" N GLN C 426 " --> pdb=" O ALA C 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.738A pdb=" N THR D 76 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE D 89 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE D 123 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LYS D 91 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE D 125 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE D 180 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE D 163 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE D 182 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLY D 226 " --> pdb=" O MET D 183 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 307 through 314 removed outlier: 6.588A pdb=" N LEU D 418 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE D 397 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR D 420 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 400 through 402 removed outlier: 6.472A pdb=" N GLN D 426 " --> pdb=" O ALA D 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.796A pdb=" N THR E 76 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE E 89 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE E 123 " --> pdb=" O PHE E 89 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LYS E 91 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE E 125 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE E 180 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE E 163 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE E 182 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY E 226 " --> pdb=" O MET E 183 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 166 through 168 removed outlier: 6.906A pdb=" N TYR E 189 " --> pdb=" O CYS E 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 307 through 314 removed outlier: 6.695A pdb=" N LEU E 418 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ILE E 397 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TYR E 420 " --> pdb=" O ILE E 397 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 400 through 402 removed outlier: 6.026A pdb=" N GLN E 426 " --> pdb=" O ALA E 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 74 through 81 removed outlier: 8.363A pdb=" N PHE F 89 " --> pdb=" O PRO F 121 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE F 123 " --> pdb=" O PHE F 89 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LYS F 91 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE F 125 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE F 180 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE F 163 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE F 182 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 166 through 168 removed outlier: 6.273A pdb=" N TYR F 189 " --> pdb=" O CYS F 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 307 through 314 removed outlier: 5.384A pdb=" N ASP F 360 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N VAL F 361 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS F 400 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU F 418 " --> pdb=" O THR F 395 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE F 397 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TYR F 420 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N ARG F 399 " --> pdb=" O TYR F 420 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 335 through 339 removed outlier: 3.798A pdb=" N VAL G 335 " --> pdb=" O THR G 396 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR G 396 " --> pdb=" O VAL G 335 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 357 through 359 removed outlier: 4.068A pdb=" N THR G 357 " --> pdb=" O GLU G 418 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU G 418 " --> pdb=" O THR G 357 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 508 through 513 removed outlier: 3.574A pdb=" N GLN G 508 " --> pdb=" O LEU G 505 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 521 through 523 Processing sheet with id= Y, first strand: chain 'G' and resid 635 through 637 removed outlier: 3.569A pdb=" N GLN G 611 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU G 630 " --> pdb=" O VAL G 609 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL G 609 " --> pdb=" O GLU G 630 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 510 through 513 Processing sheet with id= AA, first strand: chain 'H' and resid 600 through 602 removed outlier: 3.574A pdb=" N LEU H 664 " --> pdb=" O LEU H 601 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 608 through 612 removed outlier: 6.833A pdb=" N ILE H 628 " --> pdb=" O LYS H 610 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE H 612 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N LEU H 626 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU H 638 " --> pdb=" O LEU H 626 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 336 through 338 Processing sheet with id= AD, first strand: chain 'I' and resid 357 through 359 removed outlier: 3.569A pdb=" N ALA I 416 " --> pdb=" O GLN I 359 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 576 through 579 Processing sheet with id= AF, first strand: chain 'I' and resid 625 through 630 removed outlier: 6.879A pdb=" N LEU I 638 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE I 628 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN I 636 " --> pdb=" O ILE I 628 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 336 through 338 Processing sheet with id= AH, first strand: chain 'J' and resid 357 through 359 removed outlier: 3.745A pdb=" N THR J 357 " --> pdb=" O GLU J 418 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 576 through 578 Processing sheet with id= AJ, first strand: chain 'J' and resid 628 through 630 Processing sheet with id= AK, first strand: chain 'K' and resid 336 through 339 Processing sheet with id= AL, first strand: chain 'K' and resid 576 through 578 Processing sheet with id= AM, first strand: chain 'K' and resid 533 through 535 Processing sheet with id= AN, first strand: chain 'K' and resid 635 through 637 removed outlier: 5.636A pdb=" N GLU K 630 " --> pdb=" O VAL K 609 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL K 609 " --> pdb=" O GLU K 630 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 357 through 359 removed outlier: 3.607A pdb=" N THR L 357 " --> pdb=" O GLU L 418 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'L' and resid 372 through 375 removed outlier: 7.061A pdb=" N VAL L 339 " --> pdb=" O ILE L 391 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS L 393 " --> pdb=" O SER L 337 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N SER L 337 " --> pdb=" O LYS L 393 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'L' and resid 576 through 578 removed outlier: 3.709A pdb=" N GLN L 508 " --> pdb=" O LEU L 505 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'L' and resid 533 through 535 removed outlier: 3.617A pdb=" N ARG L 534 " --> pdb=" O THR L 547 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL L 548 " --> pdb=" O GLN L 551 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'L' and resid 635 through 637 removed outlier: 3.740A pdb=" N ILE L 628 " --> pdb=" O GLN L 611 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN L 611 " --> pdb=" O ILE L 628 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU L 630 " --> pdb=" O VAL L 609 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL L 609 " --> pdb=" O GLU L 630 " (cutoff:3.500A) 1313 hydrogen bonds defined for protein. 3162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.93 Time building geometry restraints manager: 14.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.81: 37050 1.81 - 2.43: 16 2.43 - 3.05: 0 3.05 - 3.67: 8 3.67 - 4.30: 4 Bond restraints: 37078 Sorted by residual: bond pdb=" AO6 COA D 601 " pdb=" AP2 COA D 601 " ideal model delta sigma weight residual 1.610 4.296 -2.686 2.00e-02 2.50e+03 1.80e+04 bond pdb=" AP1 COA D 601 " pdb="AO5* COA D 601 " ideal model delta sigma weight residual 1.610 4.233 -2.623 2.00e-02 2.50e+03 1.72e+04 bond pdb=" AP1 COA B 601 " pdb="AO5* COA B 601 " ideal model delta sigma weight residual 1.610 3.844 -2.234 2.00e-02 2.50e+03 1.25e+04 bond pdb=" AP1 COA A 601 " pdb="AO5* COA A 601 " ideal model delta sigma weight residual 1.610 3.786 -2.176 2.00e-02 2.50e+03 1.18e+04 bond pdb=" AP1 COA C 601 " pdb="AO5* COA C 601 " ideal model delta sigma weight residual 1.610 3.613 -2.003 2.00e-02 2.50e+03 1.00e+04 ... (remaining 37073 not shown) Histogram of bond angle deviations from ideal: 17.70 - 48.04: 5 48.04 - 78.38: 10 78.38 - 108.71: 2539 108.71 - 139.05: 47614 139.05 - 169.38: 10 Bond angle restraints: 50178 Sorted by residual: angle pdb=" AO3 COA D 601 " pdb=" AP2 COA D 601 " pdb=" AO6 COA D 601 " ideal model delta sigma weight residual 102.60 17.70 84.90 3.00e+00 1.11e-01 8.01e+02 angle pdb=" AO3 COA D 601 " pdb=" AP1 COA D 601 " pdb="AO5* COA D 601 " ideal model delta sigma weight residual 102.60 19.67 82.93 3.00e+00 1.11e-01 7.64e+02 angle pdb=" AO3 COA B 601 " pdb=" AP1 COA B 601 " pdb="AO5* COA B 601 " ideal model delta sigma weight residual 102.60 37.87 64.73 3.00e+00 1.11e-01 4.66e+02 angle pdb=" AO3 COA A 601 " pdb=" AP1 COA A 601 " pdb="AO5* COA A 601 " ideal model delta sigma weight residual 102.60 40.88 61.72 3.00e+00 1.11e-01 4.23e+02 angle pdb=" AO5 COA C 601 " pdb=" AP2 COA C 601 " pdb=" AO6 COA C 601 " ideal model delta sigma weight residual 109.50 169.38 -59.88 3.00e+00 1.11e-01 3.98e+02 ... (remaining 50173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 21972 35.62 - 71.23: 398 71.23 - 106.85: 48 106.85 - 142.47: 9 142.47 - 178.08: 13 Dihedral angle restraints: 22440 sinusoidal: 9137 harmonic: 13303 Sorted by residual: dihedral pdb=" AO6 COA A 601 " pdb="PC11 COA A 601 " pdb="PC12 COA A 601 " pdb="PC10 COA A 601 " ideal model delta sinusoidal sigma weight residual 291.50 113.42 178.08 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" AO3 COA A 601 " pdb=" AP1 COA A 601 " pdb="AO5* COA A 601 " pdb="AC5* COA A 601 " ideal model delta sinusoidal sigma weight residual 291.94 116.69 175.25 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" AO7 COA B 601 " pdb="AO3* COA B 601 " pdb="AP3* COA B 601 " pdb="AC3* COA B 601 " ideal model delta sinusoidal sigma weight residual -163.46 9.10 -172.56 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 22437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4355 0.061 - 0.122: 1152 0.122 - 0.183: 120 0.183 - 0.244: 3 0.244 - 0.304: 2 Chirality restraints: 5632 Sorted by residual: chirality pdb=" C2 BTI L 701 " pdb=" C4 BTI L 701 " pdb=" C7 BTI L 701 " pdb=" S1 BTI L 701 " both_signs ideal model delta sigma weight residual False 3.11 3.41 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LYS J 633 " pdb=" N LYS J 633 " pdb=" C LYS J 633 " pdb=" CB LYS J 633 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA MET G 632 " pdb=" N MET G 632 " pdb=" C MET G 632 " pdb=" CB MET G 632 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 5629 not shown) Planarity restraints: 6569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI G 701 " 0.078 2.00e-02 2.50e+03 2.06e-01 6.39e+02 pdb=" C4 BTI G 701 " -0.096 2.00e-02 2.50e+03 pdb=" C5 BTI G 701 " -0.228 2.00e-02 2.50e+03 pdb=" N2 BTI G 701 " 0.190 2.00e-02 2.50e+03 pdb=" N3 BTI G 701 " 0.302 2.00e-02 2.50e+03 pdb=" O3 BTI G 701 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI L 701 " -0.066 2.00e-02 2.50e+03 1.84e-01 5.10e+02 pdb=" C4 BTI L 701 " 0.159 2.00e-02 2.50e+03 pdb=" C5 BTI L 701 " 0.137 2.00e-02 2.50e+03 pdb=" N2 BTI L 701 " -0.237 2.00e-02 2.50e+03 pdb=" N3 BTI L 701 " -0.219 2.00e-02 2.50e+03 pdb=" O3 BTI L 701 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI J 701 " 0.065 2.00e-02 2.50e+03 1.84e-01 5.06e+02 pdb=" C4 BTI J 701 " -0.046 2.00e-02 2.50e+03 pdb=" C5 BTI J 701 " -0.231 2.00e-02 2.50e+03 pdb=" N2 BTI J 701 " 0.137 2.00e-02 2.50e+03 pdb=" N3 BTI J 701 " 0.283 2.00e-02 2.50e+03 pdb=" O3 BTI J 701 " -0.209 2.00e-02 2.50e+03 ... (remaining 6566 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 48 2.31 - 2.96: 18256 2.96 - 3.61: 48156 3.61 - 4.25: 73387 4.25 - 4.90: 128591 Nonbonded interactions: 268438 Sorted by model distance: nonbonded pdb=" AP2 COA F 601 " pdb="AO5* COA F 601 " model vdw 1.664 2.720 nonbonded pdb=" AP2 COA D 601 " pdb="AO5* COA D 601 " model vdw 1.664 2.720 nonbonded pdb=" AP2 COA C 601 " pdb="AO5* COA C 601 " model vdw 1.664 2.720 nonbonded pdb=" AP2 COA B 601 " pdb="AO5* COA B 601 " model vdw 1.666 2.720 nonbonded pdb=" AP2 COA E 601 " pdb="AO5* COA E 601 " model vdw 1.666 2.720 ... (remaining 268433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 510 or (resid 601 and (name AC2 or name AC4 or n \ ame AC5 or name AC6 or name AC8 or name AN1 or name AN3 or name AN6 or name AN7 \ or name AN9 or name AO1 or name AO2 or name AO3 or name AO4 or name AO5 or name \ AO6 or name AO7 or name AO8 or name AO9 or name AP1 or name AP2 or name AC1* or \ name AC2* or name AC3* or name AC4* or name AC5* or name AO2* or name AO3* or na \ me AO4* or name AO5* or name AP3*)))) selection = (chain 'B' and (resid 5 through 510 or (resid 601 and (name AC2 or name AC4 or n \ ame AC5 or name AC6 or name AC8 or name AN1 or name AN3 or name AN6 or name AN7 \ or name AN9 or name AO1 or name AO2 or name AO3 or name AO4 or name AO5 or name \ AO6 or name AO7 or name AO8 or name AO9 or name AP1 or name AP2 or name AC1* or \ name AC2* or name AC3* or name AC4* or name AC5* or name AO2* or name AO3* or na \ me AO4* or name AO5* or name AP3*)))) selection = (chain 'C' and (resid 5 through 510 or (resid 601 and (name AC2 or name AC4 or n \ ame AC5 or name AC6 or name AC8 or name AN1 or name AN3 or name AN6 or name AN7 \ or name AN9 or name AO1 or name AO2 or name AO3 or name AO4 or name AO5 or name \ AO6 or name AO7 or name AO8 or name AO9 or name AP1 or name AP2 or name AC1* or \ name AC2* or name AC3* or name AC4* or name AC5* or name AO2* or name AO3* or na \ me AO4* or name AO5* or name AP3*)))) selection = (chain 'D' and (resid 5 through 510 or (resid 601 and (name AC2 or name AC4 or n \ ame AC5 or name AC6 or name AC8 or name AN1 or name AN3 or name AN6 or name AN7 \ or name AN9 or name AO1 or name AO2 or name AO3 or name AO4 or name AO5 or name \ AO6 or name AO7 or name AO8 or name AO9 or name AP1 or name AP2 or name AC1* or \ name AC2* or name AC3* or name AC4* or name AC5* or name AO2* or name AO3* or na \ me AO4* or name AO5* or name AP3*)))) selection = chain 'E' selection = (chain 'F' and (resid 5 through 510 or (resid 601 and (name AC2 or name AC4 or n \ ame AC5 or name AC6 or name AC8 or name AN1 or name AN3 or name AN6 or name AN7 \ or name AN9 or name AO1 or name AO2 or name AO3 or name AO4 or name AO5 or name \ AO6 or name AO7 or name AO8 or name AO9 or name AP1 or name AP2 or name AC1* or \ name AC2* or name AC3* or name AC4* or name AC5* or name AO2* or name AO3* or na \ me AO4* or name AO5* or name AP3*)))) } ncs_group { reference = (chain 'G' and (resid 334 through 339 or resid 354 through 396 or resid 401 thro \ ugh 431 or resid 456 through 666 or resid 701)) selection = (chain 'I' and (resid 334 through 339 or resid 354 through 382 or resid 389 thro \ ugh 396 or resid 401 through 431 or resid 456 through 666 or resid 701)) selection = (chain 'J' and (resid 334 through 339 or resid 354 through 361 or resid 370 thro \ ugh 382 or resid 389 through 431 or resid 456 through 666 or resid 701)) selection = (chain 'K' and (resid 334 through 339 or resid 354 through 361 or resid 370 thro \ ugh 382 or resid 389 through 396 or resid 401 through 431 or resid 456 through 6 \ 66 or resid 701)) selection = (chain 'L' and (resid 334 through 339 or resid 354 through 382 or resid 389 thro \ ugh 396 or resid 401 through 431 or resid 456 through 666 or resid 701)) } 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: 2.020 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: 6.160 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 91.070 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.038 2.686 37078 Z= 2.959 Angle : 1.468 84.896 50178 Z= 0.604 Chirality : 0.052 0.304 5632 Planarity : 0.008 0.206 6569 Dihedral : 16.192 178.084 13886 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.10), residues: 4638 helix: -1.46 (0.11), residues: 1547 sheet: -0.75 (0.17), residues: 766 loop : -2.39 (0.11), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 537 HIS 0.008 0.002 HIS C 378 PHE 0.027 0.002 PHE B 384 TYR 0.017 0.002 TYR D 173 ARG 0.009 0.001 ARG L 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 301 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 4.408 Fit side-chains REVERT: C 177 MET cc_start: 0.8991 (mtm) cc_final: 0.8775 (mtp) REVERT: E 243 ASP cc_start: 0.8342 (m-30) cc_final: 0.7873 (t0) REVERT: E 497 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7721 (mt-10) REVERT: F 255 GLU cc_start: 0.8442 (pp20) cc_final: 0.8176 (pp20) REVERT: F 449 LYS cc_start: 0.7932 (tppp) cc_final: 0.7404 (tptp) REVERT: F 452 GLU cc_start: 0.8639 (tt0) cc_final: 0.8395 (tm-30) REVERT: I 390 MET cc_start: 0.7662 (mpp) cc_final: 0.7383 (mpp) REVERT: I 599 LYS cc_start: 0.7686 (mppt) cc_final: 0.7431 (mmtm) REVERT: I 632 MET cc_start: 0.9123 (mtt) cc_final: 0.8826 (mtt) REVERT: J 390 MET cc_start: 0.7822 (ttm) cc_final: 0.7119 (mmp) REVERT: J 589 MET cc_start: 0.8762 (mmp) cc_final: 0.8551 (mmp) REVERT: K 386 HIS cc_start: 0.7955 (m-70) cc_final: 0.7644 (m170) REVERT: K 393 LYS cc_start: 0.8211 (mttt) cc_final: 0.7692 (mtmt) REVERT: K 482 LYS cc_start: 0.8973 (ttpt) cc_final: 0.8757 (tmmt) REVERT: K 613 MET cc_start: 0.7723 (ptp) cc_final: 0.7416 (mmp) REVERT: K 634 MET cc_start: 0.7968 (ttm) cc_final: 0.7305 (tpp) REVERT: L 610 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8253 (mtpp) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.5398 time to fit residues: 257.7778 Evaluate side-chains 240 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 20.0000 chunk 351 optimal weight: 30.0000 chunk 195 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 237 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 363 optimal weight: 0.1980 chunk 140 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 270 optimal weight: 10.0000 chunk 421 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 217 HIS A 325 GLN A 349 ASN A 378 HIS A 388 GLN A 413 HIS B 57 HIS B 104 HIS B 217 HIS B 325 GLN B 378 HIS B 388 GLN C 57 HIS ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 278 ASN C 325 GLN C 388 GLN C 480 HIS D 112 GLN D 217 HIS D 278 ASN D 325 GLN D 349 ASN D 413 HIS D 480 HIS E 57 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS E 278 ASN E 388 GLN E 480 HIS F 27 GLN F 57 HIS F 104 HIS F 217 HIS F 349 ASN F 388 GLN F 480 HIS G 611 GLN H 479 ASN H 562 ASN H 618 GLN I 386 HIS I 488 GLN I 508 GLN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN J 359 GLN J 567 GLN J 622 ASN K 373 ASN L 408 GLN L 488 GLN L 498 GLN L 556 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37078 Z= 0.229 Angle : 0.608 15.954 50178 Z= 0.302 Chirality : 0.046 0.398 5632 Planarity : 0.005 0.068 6569 Dihedral : 11.553 179.742 5313 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.22 % Allowed : 14.19 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.11), residues: 4638 helix: -0.26 (0.13), residues: 1584 sheet: -0.25 (0.18), residues: 763 loop : -1.89 (0.12), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 544 HIS 0.006 0.001 HIS C 104 PHE 0.012 0.001 PHE L 578 TYR 0.013 0.001 TYR G 358 ARG 0.004 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 306 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 260 time to evaluate : 4.136 Fit side-chains revert: symmetry clash REVERT: B 127 ASP cc_start: 0.8417 (t0) cc_final: 0.7736 (t0) REVERT: C 500 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: E 243 ASP cc_start: 0.8258 (m-30) cc_final: 0.7754 (t0) REVERT: F 255 GLU cc_start: 0.8346 (pp20) cc_final: 0.8094 (pp20) REVERT: F 449 LYS cc_start: 0.7915 (tppp) cc_final: 0.7688 (tptp) REVERT: G 613 MET cc_start: 0.8674 (ptp) cc_final: 0.8366 (pmm) REVERT: G 634 MET cc_start: 0.7594 (tpp) cc_final: 0.6798 (tpp) REVERT: H 535 SER cc_start: 0.8291 (m) cc_final: 0.8063 (m) REVERT: I 599 LYS cc_start: 0.7687 (mppt) cc_final: 0.7119 (mtpt) REVERT: I 632 MET cc_start: 0.9018 (mtt) cc_final: 0.8657 (mtt) REVERT: I 634 MET cc_start: 0.7921 (tpp) cc_final: 0.7447 (tpp) REVERT: J 634 MET cc_start: 0.8345 (tpp) cc_final: 0.7987 (tpp) REVERT: K 386 HIS cc_start: 0.7963 (m-70) cc_final: 0.7685 (m170) REVERT: K 390 MET cc_start: 0.7540 (ttp) cc_final: 0.7110 (tpp) REVERT: K 393 LYS cc_start: 0.8178 (mttt) cc_final: 0.7636 (mtmt) REVERT: K 613 MET cc_start: 0.7691 (ptp) cc_final: 0.7357 (mmp) REVERT: K 634 MET cc_start: 0.8071 (ttm) cc_final: 0.7291 (tpp) REVERT: L 426 PHE cc_start: 0.7386 (t80) cc_final: 0.7179 (t80) REVERT: L 610 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8185 (ttmm) outliers start: 46 outliers final: 23 residues processed: 286 average time/residue: 0.4874 time to fit residues: 236.2943 Evaluate side-chains 262 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 4.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain H residue 506 SER Chi-restraints excluded: chain H residue 513 THR Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain K residue 373 ASN Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 422 optimal weight: 0.0270 chunk 456 optimal weight: 8.9990 chunk 375 optimal weight: 0.0770 chunk 418 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 overall best weight: 4.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 HIS B 388 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 413 HIS E 82 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 594 ASN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 37078 Z= 0.325 Angle : 0.574 8.573 50178 Z= 0.295 Chirality : 0.046 0.277 5632 Planarity : 0.005 0.053 6569 Dihedral : 10.622 177.525 5313 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.50 % Allowed : 16.53 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.12), residues: 4638 helix: -0.05 (0.13), residues: 1594 sheet: -0.20 (0.18), residues: 718 loop : -1.83 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 544 HIS 0.007 0.001 HIS C 104 PHE 0.020 0.001 PHE L 578 TYR 0.012 0.001 TYR G 358 ARG 0.004 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 339 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 245 time to evaluate : 4.324 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8045 (mmp) REVERT: B 127 ASP cc_start: 0.8458 (t0) cc_final: 0.7804 (t0) REVERT: B 177 MET cc_start: 0.8515 (mtm) cc_final: 0.8157 (mtt) REVERT: C 53 MET cc_start: 0.8599 (ttm) cc_final: 0.8175 (ttm) REVERT: C 64 MET cc_start: 0.8216 (tpp) cc_final: 0.7852 (tpp) REVERT: C 500 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: D 183 MET cc_start: 0.8579 (mtp) cc_final: 0.8304 (mtp) REVERT: D 293 GLU cc_start: 0.8493 (mp0) cc_final: 0.8150 (mp0) REVERT: D 386 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7318 (t80) REVERT: E 243 ASP cc_start: 0.8373 (m-30) cc_final: 0.7879 (t0) REVERT: F 255 GLU cc_start: 0.8280 (pp20) cc_final: 0.8045 (pp20) REVERT: F 334 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7810 (p0) REVERT: G 634 MET cc_start: 0.7352 (tpp) cc_final: 0.6596 (tpp) REVERT: H 535 SER cc_start: 0.8374 (m) cc_final: 0.8160 (m) REVERT: H 605 MET cc_start: 0.8572 (ttm) cc_final: 0.8327 (tpp) REVERT: I 578 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6663 (p90) REVERT: I 599 LYS cc_start: 0.7593 (mppt) cc_final: 0.7053 (mtpt) REVERT: I 632 MET cc_start: 0.9212 (mtt) cc_final: 0.8847 (mtt) REVERT: I 634 MET cc_start: 0.8082 (tpp) cc_final: 0.7817 (tpp) REVERT: J 634 MET cc_start: 0.8435 (tpp) cc_final: 0.8074 (tpp) REVERT: K 373 ASN cc_start: 0.8452 (p0) cc_final: 0.8198 (p0) REVERT: K 390 MET cc_start: 0.7573 (ttp) cc_final: 0.7281 (tpp) REVERT: K 393 LYS cc_start: 0.8126 (mttt) cc_final: 0.7673 (mtmt) REVERT: K 605 MET cc_start: 0.6632 (tpt) cc_final: 0.6251 (tpp) REVERT: K 613 MET cc_start: 0.7719 (ptp) cc_final: 0.7333 (mmp) REVERT: K 621 LYS cc_start: 0.4991 (mttt) cc_final: 0.4782 (mttt) REVERT: K 634 MET cc_start: 0.8118 (ttm) cc_final: 0.7279 (tpp) REVERT: K 652 LYS cc_start: 0.7932 (ptpp) cc_final: 0.7605 (ptmt) REVERT: L 610 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8228 (ttmm) REVERT: L 634 MET cc_start: 0.7216 (tpp) cc_final: 0.6786 (tpp) outliers start: 94 outliers final: 68 residues processed: 316 average time/residue: 0.4356 time to fit residues: 235.9546 Evaluate side-chains 304 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 231 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 334 ASP Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 506 SER Chi-restraints excluded: chain H residue 513 THR Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 578 PHE Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 579 THR Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 374 ASP Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 423 optimal weight: 10.0000 chunk 448 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 chunk 401 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 618 GLN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37078 Z= 0.194 Angle : 0.508 8.427 50178 Z= 0.258 Chirality : 0.044 0.271 5632 Planarity : 0.004 0.043 6569 Dihedral : 9.896 178.047 5313 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.66 % Allowed : 17.49 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 4638 helix: 0.18 (0.13), residues: 1596 sheet: 0.02 (0.19), residues: 691 loop : -1.71 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 544 HIS 0.005 0.001 HIS B 104 PHE 0.011 0.001 PHE I 578 TYR 0.015 0.001 TYR G 358 ARG 0.006 0.000 ARG D 494 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 350 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 250 time to evaluate : 4.379 Fit side-chains revert: symmetry clash REVERT: B 127 ASP cc_start: 0.8483 (t0) cc_final: 0.7857 (t0) REVERT: B 177 MET cc_start: 0.8446 (mtm) cc_final: 0.8099 (mtt) REVERT: C 53 MET cc_start: 0.8573 (ttm) cc_final: 0.8090 (ttm) REVERT: C 64 MET cc_start: 0.8147 (tpp) cc_final: 0.7820 (tpp) REVERT: C 230 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7701 (p0) REVERT: C 500 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: D 183 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8247 (mtp) REVERT: D 266 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8122 (p0) REVERT: D 293 GLU cc_start: 0.8408 (mp0) cc_final: 0.8186 (mp0) REVERT: D 386 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.7371 (t80) REVERT: E 243 ASP cc_start: 0.8316 (m-30) cc_final: 0.7812 (t0) REVERT: F 255 GLU cc_start: 0.8325 (pp20) cc_final: 0.8096 (pp20) REVERT: H 535 SER cc_start: 0.8358 (m) cc_final: 0.8103 (m) REVERT: H 605 MET cc_start: 0.8311 (ttm) cc_final: 0.8097 (tpp) REVERT: I 599 LYS cc_start: 0.7591 (mppt) cc_final: 0.7039 (mtpt) REVERT: I 632 MET cc_start: 0.9139 (mtt) cc_final: 0.8756 (mtt) REVERT: I 634 MET cc_start: 0.8086 (tpp) cc_final: 0.7796 (tpp) REVERT: J 479 ASN cc_start: 0.8721 (t0) cc_final: 0.8282 (m110) REVERT: J 634 MET cc_start: 0.8270 (tpp) cc_final: 0.7978 (tpp) REVERT: K 373 ASN cc_start: 0.8434 (p0) cc_final: 0.8130 (p0) REVERT: K 390 MET cc_start: 0.7463 (ttp) cc_final: 0.7130 (tpp) REVERT: K 393 LYS cc_start: 0.8129 (mttt) cc_final: 0.7675 (mtmt) REVERT: K 479 ASN cc_start: 0.8409 (t0) cc_final: 0.8107 (t0) REVERT: K 605 MET cc_start: 0.6783 (tpt) cc_final: 0.6422 (tpp) REVERT: K 613 MET cc_start: 0.7730 (ptp) cc_final: 0.7325 (mmp) REVERT: K 621 LYS cc_start: 0.4637 (mttt) cc_final: 0.4433 (mttp) REVERT: K 634 MET cc_start: 0.8114 (ttm) cc_final: 0.7327 (tpp) REVERT: L 359 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: L 610 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8218 (ttmm) REVERT: L 634 MET cc_start: 0.7325 (tpp) cc_final: 0.6861 (tpp) outliers start: 100 outliers final: 70 residues processed: 327 average time/residue: 0.4295 time to fit residues: 242.5681 Evaluate side-chains 313 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 237 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 334 ASP Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 506 SER Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 553 VAL Chi-restraints excluded: chain K residue 579 THR Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 374 ASP Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 333 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 382 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 402 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN B 413 HIS ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS C 278 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 ASN H 556 GLN H 562 ASN H 618 GLN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 508 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.136 37078 Z= 0.544 Angle : 0.666 8.506 50178 Z= 0.346 Chirality : 0.049 0.237 5632 Planarity : 0.005 0.052 6569 Dihedral : 9.526 177.634 5313 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.86 % Allowed : 18.23 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 4638 helix: -0.15 (0.13), residues: 1596 sheet: -0.16 (0.18), residues: 732 loop : -1.93 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 544 HIS 0.010 0.002 HIS C 104 PHE 0.028 0.002 PHE L 578 TYR 0.018 0.002 TYR E 189 ARG 0.006 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 378 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 233 time to evaluate : 4.107 Fit side-chains revert: symmetry clash REVERT: B 127 ASP cc_start: 0.8607 (t0) cc_final: 0.7983 (t0) REVERT: B 177 MET cc_start: 0.8576 (mtm) cc_final: 0.8237 (mtt) REVERT: C 64 MET cc_start: 0.8240 (tpp) cc_final: 0.7891 (tpp) REVERT: C 230 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.7939 (p0) REVERT: C 478 MET cc_start: 0.8495 (mmm) cc_final: 0.8071 (mtm) REVERT: C 500 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: D 266 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8111 (p0) REVERT: D 293 GLU cc_start: 0.8482 (mp0) cc_final: 0.8243 (mp0) REVERT: D 386 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.7439 (t80) REVERT: F 255 GLU cc_start: 0.8387 (pp20) cc_final: 0.8107 (pp20) REVERT: F 334 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8070 (p0) REVERT: G 423 ASN cc_start: 0.6391 (OUTLIER) cc_final: 0.6124 (p0) REVERT: G 634 MET cc_start: 0.7540 (tpp) cc_final: 0.6840 (tpp) REVERT: H 621 LYS cc_start: 0.6032 (mttp) cc_final: 0.5643 (tttt) REVERT: I 578 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6542 (p90) REVERT: I 599 LYS cc_start: 0.7607 (mppt) cc_final: 0.7058 (mtpt) REVERT: I 634 MET cc_start: 0.8113 (tpp) cc_final: 0.7764 (tpp) REVERT: J 613 MET cc_start: 0.6934 (mtm) cc_final: 0.6704 (mtm) REVERT: J 634 MET cc_start: 0.8384 (tpp) cc_final: 0.8048 (tpp) REVERT: K 373 ASN cc_start: 0.8324 (p0) cc_final: 0.8083 (p0) REVERT: K 390 MET cc_start: 0.7674 (ttp) cc_final: 0.7301 (tpp) REVERT: K 613 MET cc_start: 0.7727 (ptp) cc_final: 0.7323 (mmp) REVERT: L 610 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8228 (ttmm) REVERT: L 634 MET cc_start: 0.7395 (tpp) cc_final: 0.6960 (tpp) outliers start: 145 outliers final: 109 residues processed: 356 average time/residue: 0.4179 time to fit residues: 258.8999 Evaluate side-chains 340 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 224 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 334 ASP Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 334 ASP Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 423 ASN Chi-restraints excluded: chain G residue 496 THR Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 577 VAL Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain H residue 480 ILE Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 506 SER Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 513 THR Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 394 LEU Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 578 PHE Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 553 VAL Chi-restraints excluded: chain K residue 579 THR Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 374 ASP Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 557 VAL Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Chi-restraints excluded: chain L residue 588 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 8.9990 chunk 403 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 448 optimal weight: 5.9990 chunk 372 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN E 104 HIS ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 618 GLN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 37078 Z= 0.138 Angle : 0.489 7.921 50178 Z= 0.248 Chirality : 0.043 0.156 5632 Planarity : 0.004 0.041 6569 Dihedral : 8.692 169.871 5313 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.53 % Allowed : 20.04 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.12), residues: 4638 helix: 0.25 (0.13), residues: 1591 sheet: 0.16 (0.19), residues: 694 loop : -1.66 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 544 HIS 0.004 0.001 HIS B 104 PHE 0.008 0.001 PHE A 384 TYR 0.015 0.001 TYR L 358 ARG 0.003 0.000 ARG F 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 354 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 259 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.8451 (t0) cc_final: 0.7957 (t0) REVERT: B 177 MET cc_start: 0.8405 (mtm) cc_final: 0.8072 (mtt) REVERT: C 230 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7653 (p0) REVERT: C 478 MET cc_start: 0.8454 (mmm) cc_final: 0.8093 (mtm) REVERT: C 500 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: D 293 GLU cc_start: 0.8343 (mp0) cc_final: 0.8068 (mp0) REVERT: D 386 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7424 (t80) REVERT: E 118 MET cc_start: 0.8016 (mpp) cc_final: 0.7796 (mpp) REVERT: E 458 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8050 (tm-30) REVERT: F 164 MET cc_start: 0.8479 (mmm) cc_final: 0.8251 (mmm) REVERT: F 255 GLU cc_start: 0.8349 (pp20) cc_final: 0.8137 (pp20) REVERT: H 621 LYS cc_start: 0.5936 (mttp) cc_final: 0.5592 (tttt) REVERT: I 578 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6659 (p90) REVERT: I 599 LYS cc_start: 0.7678 (mppt) cc_final: 0.7111 (mtpt) REVERT: I 634 MET cc_start: 0.8162 (tpp) cc_final: 0.7882 (tpp) REVERT: J 479 ASN cc_start: 0.8682 (t0) cc_final: 0.8288 (m110) REVERT: J 634 MET cc_start: 0.8048 (tpp) cc_final: 0.7831 (tpp) REVERT: K 373 ASN cc_start: 0.8361 (p0) cc_final: 0.8103 (p0) REVERT: K 479 ASN cc_start: 0.8430 (t0) cc_final: 0.8164 (t0) REVERT: K 497 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7420 (t80) REVERT: K 605 MET cc_start: 0.6617 (tpt) cc_final: 0.6267 (tpt) REVERT: K 613 MET cc_start: 0.7739 (ptp) cc_final: 0.7317 (mmp) REVERT: K 634 MET cc_start: 0.8398 (ttm) cc_final: 0.7432 (tpp) REVERT: L 359 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: L 415 PHE cc_start: 0.8353 (t80) cc_final: 0.8037 (t80) REVERT: L 426 PHE cc_start: 0.7563 (t80) cc_final: 0.6921 (t80) REVERT: L 610 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8212 (ttmm) REVERT: L 634 MET cc_start: 0.7492 (tpp) cc_final: 0.7020 (tpp) outliers start: 95 outliers final: 69 residues processed: 334 average time/residue: 0.4476 time to fit residues: 255.1974 Evaluate side-chains 319 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 244 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 334 ASP Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 632 MET Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 562 ASN Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 578 PHE Chi-restraints excluded: chain J residue 426 PHE Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 497 PHE Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 374 ASP Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 377 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 447 optimal weight: 6.9990 chunk 279 optimal weight: 0.0470 chunk 272 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 618 GLN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 562 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 37078 Z= 0.368 Angle : 0.567 7.126 50178 Z= 0.292 Chirality : 0.045 0.202 5632 Planarity : 0.005 0.070 6569 Dihedral : 8.497 171.622 5313 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.57 % Allowed : 19.67 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.12), residues: 4638 helix: 0.13 (0.13), residues: 1598 sheet: 0.03 (0.18), residues: 744 loop : -1.72 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 544 HIS 0.005 0.001 HIS F 480 PHE 0.022 0.001 PHE L 578 TYR 0.013 0.001 TYR E 189 ARG 0.004 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 370 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 236 time to evaluate : 4.662 Fit side-chains revert: symmetry clash REVERT: B 127 ASP cc_start: 0.8538 (t0) cc_final: 0.8053 (t0) REVERT: B 177 MET cc_start: 0.8535 (mtm) cc_final: 0.8176 (mtt) REVERT: B 492 MET cc_start: 0.8691 (ttp) cc_final: 0.8232 (tmm) REVERT: C 53 MET cc_start: 0.8605 (ttp) cc_final: 0.8380 (ttm) REVERT: C 230 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7843 (p0) REVERT: C 478 MET cc_start: 0.8485 (mmm) cc_final: 0.8119 (mtm) REVERT: D 386 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.7510 (t80) REVERT: E 173 TYR cc_start: 0.8525 (m-80) cc_final: 0.8244 (m-10) REVERT: E 458 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8082 (tm-30) REVERT: F 255 GLU cc_start: 0.8361 (pp20) cc_final: 0.8119 (pp20) REVERT: F 334 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7784 (p0) REVERT: H 621 LYS cc_start: 0.5987 (mttp) cc_final: 0.5602 (tttt) REVERT: I 478 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7509 (mt) REVERT: I 517 ASP cc_start: 0.5045 (OUTLIER) cc_final: 0.4679 (t0) REVERT: I 578 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6536 (p90) REVERT: I 599 LYS cc_start: 0.7590 (mppt) cc_final: 0.7032 (mtpt) REVERT: I 634 MET cc_start: 0.8130 (tpp) cc_final: 0.7760 (tpp) REVERT: J 634 MET cc_start: 0.8300 (tpp) cc_final: 0.8044 (tpp) REVERT: K 373 ASN cc_start: 0.8338 (p0) cc_final: 0.8131 (p0) REVERT: K 605 MET cc_start: 0.6680 (tpt) cc_final: 0.6299 (tpt) REVERT: K 613 MET cc_start: 0.7742 (ptp) cc_final: 0.7324 (mmp) REVERT: K 634 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7207 (tpp) REVERT: L 359 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: L 610 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8108 (ttmm) REVERT: L 634 MET cc_start: 0.7383 (tpp) cc_final: 0.6947 (tpp) outliers start: 134 outliers final: 106 residues processed: 350 average time/residue: 0.4215 time to fit residues: 256.9152 Evaluate side-chains 348 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 234 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 334 ASP Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 334 ASP Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 577 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 513 THR Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 543 VAL Chi-restraints excluded: chain I residue 355 LEU Chi-restraints excluded: chain I residue 412 LEU Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 517 ASP Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 578 PHE Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 426 PHE Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 553 VAL Chi-restraints excluded: chain K residue 579 THR Chi-restraints excluded: chain K residue 634 MET Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 374 ASP Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 562 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Chi-restraints excluded: chain L residue 588 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 9.9990 chunk 178 optimal weight: 0.5980 chunk 267 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 284 optimal weight: 0.5980 chunk 304 optimal weight: 9.9990 chunk 221 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 476 HIS H 562 ASN H 618 GLN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 37078 Z= 0.124 Angle : 0.477 7.365 50178 Z= 0.240 Chirality : 0.043 0.180 5632 Planarity : 0.004 0.053 6569 Dihedral : 7.952 165.408 5313 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.61 % Allowed : 20.95 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.12), residues: 4638 helix: 0.37 (0.13), residues: 1598 sheet: 0.27 (0.19), residues: 698 loop : -1.53 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 544 HIS 0.005 0.001 HIS B 104 PHE 0.008 0.001 PHE D 347 TYR 0.014 0.001 TYR L 358 ARG 0.004 0.000 ARG F 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 355 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 257 time to evaluate : 4.272 Fit side-chains revert: symmetry clash REVERT: B 127 ASP cc_start: 0.8479 (t0) cc_final: 0.8025 (t0) REVERT: B 177 MET cc_start: 0.8284 (mtm) cc_final: 0.8011 (mtt) REVERT: B 492 MET cc_start: 0.8630 (ttp) cc_final: 0.8133 (tmm) REVERT: C 53 MET cc_start: 0.8543 (ttp) cc_final: 0.8187 (ttm) REVERT: C 230 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7545 (p0) REVERT: C 478 MET cc_start: 0.8446 (mmm) cc_final: 0.8096 (mtm) REVERT: D 386 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7466 (t80) REVERT: E 118 MET cc_start: 0.7905 (mpp) cc_final: 0.7598 (mpp) REVERT: E 458 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8077 (tm-30) REVERT: F 255 GLU cc_start: 0.8332 (pp20) cc_final: 0.8118 (pp20) REVERT: F 334 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7219 (p0) REVERT: G 390 MET cc_start: 0.6647 (tmm) cc_final: 0.6291 (tmm) REVERT: H 535 SER cc_start: 0.8464 (m) cc_final: 0.8151 (m) REVERT: H 621 LYS cc_start: 0.5932 (mttp) cc_final: 0.5593 (tttt) REVERT: I 357 THR cc_start: 0.8618 (m) cc_final: 0.8080 (p) REVERT: I 578 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6461 (p90) REVERT: I 599 LYS cc_start: 0.7716 (mppt) cc_final: 0.7172 (mtpt) REVERT: I 634 MET cc_start: 0.8122 (tpp) cc_final: 0.7830 (tpp) REVERT: I 652 LYS cc_start: 0.8255 (tptt) cc_final: 0.7554 (pttm) REVERT: J 479 ASN cc_start: 0.8763 (t0) cc_final: 0.8337 (m110) REVERT: K 373 ASN cc_start: 0.8383 (p0) cc_final: 0.8172 (p0) REVERT: K 390 MET cc_start: 0.8070 (tpp) cc_final: 0.7817 (tpp) REVERT: K 479 ASN cc_start: 0.8418 (t0) cc_final: 0.7829 (t0) REVERT: K 605 MET cc_start: 0.6754 (tpt) cc_final: 0.6344 (tpt) REVERT: K 613 MET cc_start: 0.7776 (ptp) cc_final: 0.7347 (mmp) REVERT: K 634 MET cc_start: 0.8365 (ttm) cc_final: 0.7639 (tpp) REVERT: L 359 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: L 415 PHE cc_start: 0.8337 (t80) cc_final: 0.8079 (t80) REVERT: L 426 PHE cc_start: 0.7758 (t80) cc_final: 0.7187 (t80) REVERT: L 610 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8198 (ttmm) REVERT: L 634 MET cc_start: 0.7511 (tpp) cc_final: 0.7061 (tpp) outliers start: 98 outliers final: 81 residues processed: 339 average time/residue: 0.4747 time to fit residues: 279.2835 Evaluate side-chains 331 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 245 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 334 ASP Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 334 ASP Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 562 ASN Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 578 PHE Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 374 ASP Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Chi-restraints excluded: chain L residue 588 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 9.9990 chunk 428 optimal weight: 8.9990 chunk 390 optimal weight: 5.9990 chunk 416 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 327 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 376 optimal weight: 0.2980 chunk 394 optimal weight: 5.9990 chunk 415 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 278 ASN D 57 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 618 GLN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 562 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 37078 Z= 0.151 Angle : 0.480 7.155 50178 Z= 0.242 Chirality : 0.042 0.171 5632 Planarity : 0.004 0.054 6569 Dihedral : 7.661 165.450 5313 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.82 % Allowed : 20.87 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.12), residues: 4638 helix: 0.42 (0.13), residues: 1604 sheet: 0.40 (0.19), residues: 694 loop : -1.48 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 544 HIS 0.004 0.001 HIS C 104 PHE 0.011 0.001 PHE L 578 TYR 0.012 0.001 TYR L 358 ARG 0.003 0.000 ARG F 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 354 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 248 time to evaluate : 4.355 Fit side-chains revert: symmetry clash REVERT: B 127 ASP cc_start: 0.8503 (t0) cc_final: 0.8057 (t0) REVERT: B 177 MET cc_start: 0.8332 (mtm) cc_final: 0.8053 (mtt) REVERT: B 492 MET cc_start: 0.8613 (ttp) cc_final: 0.8268 (tmm) REVERT: C 230 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7567 (p0) REVERT: C 478 MET cc_start: 0.8436 (mmm) cc_final: 0.8108 (mtm) REVERT: D 64 MET cc_start: 0.8044 (tpp) cc_final: 0.7714 (ttt) REVERT: E 118 MET cc_start: 0.8000 (mpp) cc_final: 0.7773 (mpp) REVERT: E 458 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8061 (tm-30) REVERT: F 255 GLU cc_start: 0.8300 (pp20) cc_final: 0.8078 (pp20) REVERT: H 535 SER cc_start: 0.8487 (m) cc_final: 0.8149 (m) REVERT: H 605 MET cc_start: 0.8346 (ttm) cc_final: 0.8133 (tpp) REVERT: H 621 LYS cc_start: 0.6028 (mttp) cc_final: 0.5624 (ttmm) REVERT: I 357 THR cc_start: 0.8623 (m) cc_final: 0.8079 (p) REVERT: I 578 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6637 (p90) REVERT: I 599 LYS cc_start: 0.7742 (mppt) cc_final: 0.7149 (mtpt) REVERT: I 634 MET cc_start: 0.8111 (tpp) cc_final: 0.7787 (tpp) REVERT: I 652 LYS cc_start: 0.8248 (tptt) cc_final: 0.7520 (pttm) REVERT: J 479 ASN cc_start: 0.8764 (t0) cc_final: 0.8341 (m110) REVERT: J 634 MET cc_start: 0.8209 (tpp) cc_final: 0.8008 (tpp) REVERT: K 479 ASN cc_start: 0.8432 (t0) cc_final: 0.7811 (t0) REVERT: K 605 MET cc_start: 0.6772 (tpt) cc_final: 0.6367 (tpt) REVERT: K 613 MET cc_start: 0.7788 (ptp) cc_final: 0.7359 (mmp) REVERT: K 634 MET cc_start: 0.8368 (ttm) cc_final: 0.7626 (tpp) REVERT: L 359 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: L 393 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8274 (mmtm) REVERT: L 415 PHE cc_start: 0.8376 (t80) cc_final: 0.8109 (t80) REVERT: L 426 PHE cc_start: 0.7727 (t80) cc_final: 0.7149 (t80) REVERT: L 610 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8160 (ttmm) REVERT: L 634 MET cc_start: 0.7101 (tpp) cc_final: 0.6651 (tpp) outliers start: 106 outliers final: 90 residues processed: 334 average time/residue: 0.4248 time to fit residues: 245.9753 Evaluate side-chains 338 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 244 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 334 ASP Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 562 ASN Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 578 PHE Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 374 ASP Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Chi-restraints excluded: chain L residue 588 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 0.0030 chunk 440 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 209 optimal weight: 0.0470 chunk 306 optimal weight: 0.0980 chunk 462 optimal weight: 40.0000 chunk 425 optimal weight: 10.0000 chunk 368 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 284 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 overall best weight: 0.5890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN C 278 ASN E 388 GLN ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN ** H 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 618 GLN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 373 ASN K 562 ASN L 562 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 37078 Z= 0.114 Angle : 0.467 7.264 50178 Z= 0.234 Chirality : 0.042 0.159 5632 Planarity : 0.004 0.045 6569 Dihedral : 7.342 162.255 5313 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.37 % Allowed : 21.45 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4638 helix: 0.51 (0.13), residues: 1604 sheet: 0.56 (0.19), residues: 703 loop : -1.39 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 544 HIS 0.004 0.001 HIS C 104 PHE 0.007 0.001 PHE D 89 TYR 0.013 0.001 TYR L 358 ARG 0.003 0.000 ARG F 305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 348 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 259 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 113 ASP cc_start: 0.8386 (t0) cc_final: 0.7832 (t0) REVERT: B 127 ASP cc_start: 0.8471 (t0) cc_final: 0.8034 (t0) REVERT: C 230 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7656 (p0) REVERT: C 478 MET cc_start: 0.8417 (mmm) cc_final: 0.8094 (mtm) REVERT: E 118 MET cc_start: 0.7925 (mpp) cc_final: 0.7581 (mpp) REVERT: E 173 TYR cc_start: 0.8413 (m-80) cc_final: 0.8148 (m-10) REVERT: E 409 MET cc_start: 0.9393 (mmm) cc_final: 0.8965 (mmt) REVERT: E 458 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8042 (tm-30) REVERT: F 255 GLU cc_start: 0.8263 (pp20) cc_final: 0.8050 (pp20) REVERT: F 334 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7143 (p0) REVERT: G 589 MET cc_start: 0.7692 (mmm) cc_final: 0.7381 (mmm) REVERT: H 535 SER cc_start: 0.8452 (m) cc_final: 0.8099 (m) REVERT: I 357 THR cc_start: 0.8618 (m) cc_final: 0.8111 (p) REVERT: I 578 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6702 (p90) REVERT: I 599 LYS cc_start: 0.7725 (mppt) cc_final: 0.7490 (mmtm) REVERT: I 634 MET cc_start: 0.8116 (tpp) cc_final: 0.7796 (tpp) REVERT: I 652 LYS cc_start: 0.8218 (tptt) cc_final: 0.7505 (pttm) REVERT: J 479 ASN cc_start: 0.8773 (t0) cc_final: 0.8398 (m110) REVERT: J 634 MET cc_start: 0.8177 (tpp) cc_final: 0.7948 (tpp) REVERT: K 390 MET cc_start: 0.8070 (tpp) cc_final: 0.7816 (tpp) REVERT: K 479 ASN cc_start: 0.8397 (t0) cc_final: 0.8105 (t0) REVERT: K 605 MET cc_start: 0.6775 (tpt) cc_final: 0.6340 (tpt) REVERT: K 613 MET cc_start: 0.7748 (ptp) cc_final: 0.7287 (mmp) REVERT: K 634 MET cc_start: 0.8327 (ttm) cc_final: 0.7743 (tpp) REVERT: L 359 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: L 393 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8131 (mmtm) REVERT: L 415 PHE cc_start: 0.8310 (t80) cc_final: 0.8061 (t80) REVERT: L 426 PHE cc_start: 0.7553 (t80) cc_final: 0.6977 (t80) REVERT: L 610 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8184 (ttmm) REVERT: L 634 MET cc_start: 0.7086 (tpp) cc_final: 0.6643 (tpp) outliers start: 89 outliers final: 78 residues processed: 332 average time/residue: 0.4248 time to fit residues: 244.4728 Evaluate side-chains 329 residues out of total 3757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 246 time to evaluate : 4.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 334 ASP Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 334 ASP Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 578 PHE Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 373 ASN Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 374 ASP Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 562 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Chi-restraints excluded: chain L residue 588 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 10.0000 chunk 392 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 339 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 378 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN H 562 ASN H 618 GLN ** I 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 373 ASN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 562 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.070679 restraints weight = 68970.649| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.70 r_work: 0.2791 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 37078 Z= 0.462 Angle : 0.628 8.672 50178 Z= 0.325 Chirality : 0.047 0.188 5632 Planarity : 0.005 0.053 6569 Dihedral : 7.572 167.365 5313 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.82 % Allowed : 21.29 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.12), residues: 4638 helix: 0.21 (0.13), residues: 1598 sheet: 0.31 (0.19), residues: 734 loop : -1.64 (0.12), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 544 HIS 0.008 0.001 HIS F 480 PHE 0.028 0.002 PHE L 578 TYR 0.012 0.002 TYR E 386 ARG 0.006 0.001 ARG J 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6720.54 seconds wall clock time: 123 minutes 3.55 seconds (7383.55 seconds total)