Starting phenix.real_space_refine on Thu Feb 22 20:05:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp8_30147/02_2024/7bp8_30147_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp8_30147/02_2024/7bp8_30147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp8_30147/02_2024/7bp8_30147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp8_30147/02_2024/7bp8_30147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp8_30147/02_2024/7bp8_30147_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp8_30147/02_2024/7bp8_30147_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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 24 5.49 5 S 180 5.16 5 C 21996 2.51 5 N 6246 2.21 5 O 6744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E GLU 673": "OE1" <-> "OE2" Residue "E ARG 711": "NH1" <-> "NH2" Residue "E ARG 713": "NH1" <-> "NH2" Residue "E ARG 766": "NH1" <-> "NH2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F GLU 366": "OE1" <-> "OE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F GLU 556": "OE1" <-> "OE2" Residue "F GLU 673": "OE1" <-> "OE2" Residue "F ARG 711": "NH1" <-> "NH2" Residue "F ARG 713": "NH1" <-> "NH2" Residue "F ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35190 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "C" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "D" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "E" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "F" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5811 Classifications: {'peptide': 740} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.66, per 1000 atoms: 0.47 Number of scatterers: 35190 At special positions: 0 Unit cell: (167.99, 178.69, 101.65, 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 180 16.00 P 24 15.00 O 6744 8.00 N 6246 7.00 C 21996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.97 Conformation dependent library (CDL) restraints added in 5.9 seconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 42 sheets defined 39.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.54 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 131 through 138 removed outlier: 4.271A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.706A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 320 through 335 removed outlier: 3.772A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.943A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 663 removed outlier: 4.036A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 710 Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.439A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 131 through 138 removed outlier: 4.272A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.708A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.770A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.941A pdb=" N GLU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 663 removed outlier: 4.037A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 710 Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.440A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 131 through 138 removed outlier: 4.272A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.705A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 320 through 335 removed outlier: 3.769A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 424 Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.941A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 501 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 592 through 594 No H-bonds generated for 'chain 'C' and resid 592 through 594' Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 663 removed outlier: 4.036A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 710 Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.441A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 760 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 131 through 138 removed outlier: 4.281A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.707A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 320 through 335 removed outlier: 3.771A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 424 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.942A pdb=" N GLU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 592 through 594 No H-bonds generated for 'chain 'D' and resid 592 through 594' Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 663 removed outlier: 4.036A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 710 Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.440A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 131 through 138 removed outlier: 4.281A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.708A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 320 through 335 removed outlier: 3.770A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 424 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 483 through 498 removed outlier: 3.941A pdb=" N GLU E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 501 through 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 557 through 568 Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 592 through 594 No H-bonds generated for 'chain 'E' and resid 592 through 594' Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 663 removed outlier: 4.038A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 710 Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.440A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 131 through 138 removed outlier: 4.277A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.706A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 320 through 335 removed outlier: 3.769A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 424 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 483 through 498 removed outlier: 3.942A pdb=" N GLU F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 501 through 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 557 through 568 Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 592 through 594 No H-bonds generated for 'chain 'F' and resid 592 through 594' Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 663 removed outlier: 4.037A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 710 Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.440A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 29 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.929A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU A 41 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 72 " --> pdb=" O LEU A 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 66 through 69 Processing sheet with id= D, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= E, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.950A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.731A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.817A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 27 through 29 Processing sheet with id= I, first strand: chain 'B' and resid 38 through 41 removed outlier: 6.929A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 66 through 69 Processing sheet with id= K, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= L, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.952A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.729A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.819A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 27 through 29 Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 6.930A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 66 through 69 Processing sheet with id= R, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= S, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.952A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.731A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.819A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 27 through 29 Processing sheet with id= W, first strand: chain 'D' and resid 38 through 41 removed outlier: 6.930A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 66 through 69 Processing sheet with id= Y, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= Z, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.950A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.731A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.817A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 27 through 29 Processing sheet with id= AD, first strand: chain 'E' and resid 38 through 41 removed outlier: 6.929A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 66 through 69 Processing sheet with id= AF, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= AG, first strand: chain 'E' and resid 151 through 156 removed outlier: 6.952A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.730A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.820A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 27 through 29 Processing sheet with id= AK, first strand: chain 'F' and resid 38 through 41 removed outlier: 6.930A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'F' and resid 66 through 69 Processing sheet with id= AM, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AN, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.952A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 365 through 368 removed outlier: 8.731A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.819A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3132 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: 13.34 Time building geometry restraints manager: 13.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10544 1.34 - 1.46: 5809 1.46 - 1.58: 19077 1.58 - 1.70: 54 1.70 - 1.82: 288 Bond restraints: 35772 Sorted by residual: bond pdb=" C LYS E 136 " pdb=" N PRO E 137 " ideal model delta sigma weight residual 1.337 1.396 -0.059 1.11e-02 8.12e+03 2.83e+01 bond pdb=" C LYS F 136 " pdb=" N PRO F 137 " ideal model delta sigma weight residual 1.337 1.396 -0.059 1.11e-02 8.12e+03 2.83e+01 bond pdb=" C LYS B 136 " pdb=" N PRO B 137 " ideal model delta sigma weight residual 1.337 1.395 -0.059 1.11e-02 8.12e+03 2.82e+01 bond pdb=" C LYS C 136 " pdb=" N PRO C 137 " ideal model delta sigma weight residual 1.337 1.395 -0.058 1.11e-02 8.12e+03 2.74e+01 bond pdb=" C LYS D 136 " pdb=" N PRO D 137 " ideal model delta sigma weight residual 1.337 1.393 -0.057 1.11e-02 8.12e+03 2.63e+01 ... (remaining 35767 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.94: 1104 105.94 - 113.82: 19236 113.82 - 121.69: 18921 121.69 - 129.57: 8930 129.57 - 137.44: 163 Bond angle restraints: 48354 Sorted by residual: angle pdb=" C LYS B 136 " pdb=" N PRO B 137 " pdb=" CA PRO B 137 " ideal model delta sigma weight residual 119.87 126.51 -6.64 1.04e+00 9.25e-01 4.08e+01 angle pdb=" C LYS A 136 " pdb=" N PRO A 137 " pdb=" CA PRO A 137 " ideal model delta sigma weight residual 119.87 126.35 -6.48 1.04e+00 9.25e-01 3.89e+01 angle pdb=" C LYS F 136 " pdb=" N PRO F 137 " pdb=" CA PRO F 137 " ideal model delta sigma weight residual 119.87 126.14 -6.27 1.04e+00 9.25e-01 3.64e+01 angle pdb=" C LYS D 136 " pdb=" N PRO D 137 " pdb=" CA PRO D 137 " ideal model delta sigma weight residual 119.87 126.11 -6.24 1.04e+00 9.25e-01 3.60e+01 angle pdb=" C LYS C 136 " pdb=" N PRO C 137 " pdb=" CA PRO C 137 " ideal model delta sigma weight residual 119.87 125.87 -6.00 1.04e+00 9.25e-01 3.33e+01 ... (remaining 48349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.40: 21771 33.40 - 66.80: 357 66.80 - 100.21: 66 100.21 - 133.61: 12 133.61 - 167.01: 12 Dihedral angle restraints: 22218 sinusoidal: 9420 harmonic: 12798 Sorted by residual: dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual 300.00 132.99 167.01 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP C 901 " pdb=" O3A ADP C 901 " pdb=" PB ADP C 901 " pdb=" PA ADP C 901 " ideal model delta sinusoidal sigma weight residual 300.00 133.01 166.99 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual 300.00 133.03 166.97 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 22215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4466 0.098 - 0.196: 794 0.196 - 0.293: 122 0.293 - 0.391: 24 0.391 - 0.489: 12 Chirality restraints: 5418 Sorted by residual: chirality pdb=" CB ILE F 102 " pdb=" CA ILE F 102 " pdb=" CG1 ILE F 102 " pdb=" CG2 ILE F 102 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CB ILE C 102 " pdb=" CA ILE C 102 " pdb=" CG1 ILE C 102 " pdb=" CG2 ILE C 102 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CB ILE E 102 " pdb=" CA ILE E 102 " pdb=" CG1 ILE E 102 " pdb=" CG2 ILE E 102 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.88e+00 ... (remaining 5415 not shown) Planarity restraints: 6372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 189 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C ILE C 189 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE C 189 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS C 190 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 189 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C ILE E 189 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE E 189 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS E 190 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 189 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ILE F 189 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE F 189 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS F 190 " 0.020 2.00e-02 2.50e+03 ... (remaining 6369 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 9701 2.83 - 3.35: 33130 3.35 - 3.87: 56164 3.87 - 4.38: 63415 4.38 - 4.90: 107540 Nonbonded interactions: 269950 Sorted by model distance: nonbonded pdb=" O SER B 555 " pdb=" OG SER B 555 " model vdw 2.313 2.440 nonbonded pdb=" O SER E 555 " pdb=" OG SER E 555 " model vdw 2.313 2.440 nonbonded pdb=" O SER D 555 " pdb=" OG SER D 555 " model vdw 2.314 2.440 nonbonded pdb=" O SER A 555 " pdb=" OG SER A 555 " model vdw 2.314 2.440 nonbonded pdb=" O SER C 555 " pdb=" OG SER C 555 " model vdw 2.314 2.440 ... (remaining 269945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 3.960 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 84.570 Find NCS groups from input model: 2.410 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 35772 Z= 0.536 Angle : 1.380 11.890 48354 Z= 0.782 Chirality : 0.082 0.489 5418 Planarity : 0.008 0.068 6372 Dihedral : 15.249 167.011 13914 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.18 % Allowed : 3.01 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.11), residues: 4416 helix: -1.66 (0.10), residues: 1806 sheet: -1.69 (0.17), residues: 642 loop : -2.64 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 454 HIS 0.008 0.002 HIS E 183 PHE 0.035 0.004 PHE B 131 TYR 0.028 0.004 TYR B 644 ARG 0.013 0.001 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 627 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7285 (mmtt) REVERT: A 275 MET cc_start: 0.7733 (mmm) cc_final: 0.7447 (mtp) REVERT: A 351 ASN cc_start: 0.7113 (p0) cc_final: 0.6656 (p0) REVERT: B 231 LYS cc_start: 0.7670 (mmmt) cc_final: 0.7336 (mmtt) REVERT: B 239 ARG cc_start: 0.6867 (ptp-110) cc_final: 0.6510 (mtm180) REVERT: B 275 MET cc_start: 0.7914 (mmm) cc_final: 0.7695 (mtp) REVERT: B 327 GLN cc_start: 0.8487 (tp-100) cc_final: 0.8174 (tp-100) REVERT: B 351 ASN cc_start: 0.7242 (p0) cc_final: 0.6776 (p0) REVERT: B 420 LEU cc_start: 0.8920 (mt) cc_final: 0.8696 (mt) REVERT: C 239 ARG cc_start: 0.7131 (ptp-110) cc_final: 0.6723 (mtm180) REVERT: C 351 ASN cc_start: 0.7265 (p0) cc_final: 0.7047 (p0) REVERT: D 231 LYS cc_start: 0.7615 (mmmt) cc_final: 0.7254 (mmtt) REVERT: D 239 ARG cc_start: 0.6964 (ptp-110) cc_final: 0.6494 (mtt90) REVERT: D 275 MET cc_start: 0.7720 (mmm) cc_final: 0.7430 (mtp) REVERT: D 351 ASN cc_start: 0.7158 (p0) cc_final: 0.6726 (p0) REVERT: D 508 MET cc_start: 0.7970 (ttp) cc_final: 0.7666 (ttp) REVERT: E 80 GLU cc_start: 0.6165 (pm20) cc_final: 0.5478 (mp0) REVERT: E 231 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7347 (mmtt) REVERT: E 239 ARG cc_start: 0.6839 (ptp-110) cc_final: 0.6507 (mtm180) REVERT: E 327 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8111 (tp-100) REVERT: E 351 ASN cc_start: 0.7242 (p0) cc_final: 0.6898 (p0) REVERT: E 508 MET cc_start: 0.7761 (ttp) cc_final: 0.7539 (ttp) REVERT: F 239 ARG cc_start: 0.7144 (ptp-110) cc_final: 0.6731 (mtm180) REVERT: F 351 ASN cc_start: 0.7272 (p0) cc_final: 0.7025 (p0) outliers start: 7 outliers final: 0 residues processed: 633 average time/residue: 0.5817 time to fit residues: 560.7532 Evaluate side-chains 353 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 10.0000 chunk 336 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 227 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 348 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 403 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN A 458 GLN A 460 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN B 443 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN C 348 ASN C 443 ASN C 460 ASN C 538 ASN C 660 ASN C 735 HIS D 443 ASN D 458 GLN D 460 ASN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 443 ASN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN F 348 ASN F 443 ASN F 460 ASN ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN F 735 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35772 Z= 0.283 Angle : 0.684 11.337 48354 Z= 0.330 Chirality : 0.047 0.179 5418 Planarity : 0.005 0.052 6372 Dihedral : 11.322 156.969 4968 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.72 % Allowed : 9.98 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.04 (0.12), residues: 4416 helix: -0.54 (0.12), residues: 1806 sheet: -1.47 (0.17), residues: 714 loop : -2.04 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 454 HIS 0.004 0.001 HIS D 404 PHE 0.008 0.001 PHE E 131 TYR 0.032 0.002 TYR D 203 ARG 0.007 0.001 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 389 time to evaluate : 4.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7225 (tp) cc_final: 0.6903 (tt) REVERT: A 96 LEU cc_start: 0.8979 (tt) cc_final: 0.8728 (tt) REVERT: A 115 HIS cc_start: 0.5769 (OUTLIER) cc_final: 0.5412 (t70) REVERT: A 239 ARG cc_start: 0.6951 (ptp-110) cc_final: 0.6716 (mtt90) REVERT: A 275 MET cc_start: 0.7829 (mmm) cc_final: 0.7564 (mtp) REVERT: B 327 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8170 (tp-100) REVERT: B 332 MET cc_start: 0.8663 (mmm) cc_final: 0.8324 (mmm) REVERT: C 239 ARG cc_start: 0.7218 (ptp-110) cc_final: 0.6840 (mtm180) REVERT: C 327 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8026 (tp-100) REVERT: C 332 MET cc_start: 0.8803 (mmm) cc_final: 0.8518 (mmm) REVERT: C 473 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7546 (mm-40) REVERT: D 58 LEU cc_start: 0.7295 (tp) cc_final: 0.6940 (tt) REVERT: D 115 HIS cc_start: 0.5855 (OUTLIER) cc_final: 0.5476 (t70) REVERT: D 239 ARG cc_start: 0.6995 (ptp-110) cc_final: 0.6788 (mtt90) REVERT: D 275 MET cc_start: 0.7867 (mmm) cc_final: 0.7651 (mtp) REVERT: E 327 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8132 (tp-100) REVERT: F 239 ARG cc_start: 0.7206 (ptp-110) cc_final: 0.6846 (mtm180) REVERT: F 327 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8055 (tp-100) REVERT: F 473 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7535 (mm-40) outliers start: 65 outliers final: 51 residues processed: 438 average time/residue: 0.4779 time to fit residues: 334.4485 Evaluate side-chains 381 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 328 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 732 ARG Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 732 ARG Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 732 ARG Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 732 ARG Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 30.0000 chunk 125 optimal weight: 2.9990 chunk 335 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 403 optimal weight: 9.9990 chunk 436 optimal weight: 20.0000 chunk 359 optimal weight: 10.0000 chunk 400 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 324 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN F 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35772 Z= 0.269 Angle : 0.647 8.926 48354 Z= 0.311 Chirality : 0.046 0.171 5418 Planarity : 0.004 0.054 6372 Dihedral : 10.529 136.344 4968 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.27 % Allowed : 13.84 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.50 (0.12), residues: 4416 helix: -0.08 (0.12), residues: 1812 sheet: -1.04 (0.19), residues: 714 loop : -1.83 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 454 HIS 0.005 0.001 HIS B 115 PHE 0.011 0.001 PHE F 363 TYR 0.024 0.002 TYR B 244 ARG 0.009 0.001 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 351 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8961 (tt) cc_final: 0.8754 (tt) REVERT: A 115 HIS cc_start: 0.5895 (OUTLIER) cc_final: 0.5606 (t70) REVERT: A 239 ARG cc_start: 0.7014 (ptp-110) cc_final: 0.6683 (mtt90) REVERT: A 270 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8900 (p0) REVERT: B 115 HIS cc_start: 0.5818 (OUTLIER) cc_final: 0.5553 (t70) REVERT: B 351 ASN cc_start: 0.7473 (p0) cc_final: 0.7150 (p0) REVERT: C 115 HIS cc_start: 0.5439 (OUTLIER) cc_final: 0.5012 (t70) REVERT: C 239 ARG cc_start: 0.7208 (ptp-110) cc_final: 0.6842 (mtm180) REVERT: C 327 GLN cc_start: 0.8467 (tp-100) cc_final: 0.7983 (tp-100) REVERT: C 332 MET cc_start: 0.8829 (mmm) cc_final: 0.8601 (mmm) REVERT: C 473 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7507 (mm-40) REVERT: D 115 HIS cc_start: 0.5924 (OUTLIER) cc_final: 0.5624 (t70) REVERT: D 239 ARG cc_start: 0.6999 (ptp-110) cc_final: 0.6640 (mtm-85) REVERT: D 270 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8893 (p0) REVERT: E 115 HIS cc_start: 0.5781 (OUTLIER) cc_final: 0.5578 (t70) REVERT: E 327 GLN cc_start: 0.8534 (tp-100) cc_final: 0.8183 (tp-100) REVERT: F 115 HIS cc_start: 0.5610 (OUTLIER) cc_final: 0.5208 (t70) REVERT: F 239 ARG cc_start: 0.7177 (ptp-110) cc_final: 0.6824 (mtm180) REVERT: F 327 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8012 (tp-100) REVERT: F 473 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7528 (mm-40) outliers start: 86 outliers final: 57 residues processed: 417 average time/residue: 0.4782 time to fit residues: 321.1505 Evaluate side-chains 385 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 320 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 732 ARG Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 732 ARG Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 732 ARG Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 20.0000 chunk 303 optimal weight: 30.0000 chunk 209 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 192 optimal weight: 0.6980 chunk 271 optimal weight: 5.9990 chunk 405 optimal weight: 9.9990 chunk 429 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 384 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35772 Z= 0.270 Angle : 0.631 12.107 48354 Z= 0.302 Chirality : 0.046 0.186 5418 Planarity : 0.004 0.057 6372 Dihedral : 9.880 130.821 4968 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.75 % Allowed : 15.45 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.24 (0.12), residues: 4416 helix: 0.13 (0.12), residues: 1812 sheet: -0.87 (0.19), residues: 714 loop : -1.69 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 454 HIS 0.003 0.001 HIS B 115 PHE 0.017 0.001 PHE F 363 TYR 0.021 0.002 TYR B 244 ARG 0.015 0.001 ARG F 662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 338 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.5949 (OUTLIER) cc_final: 0.5674 (t70) REVERT: A 239 ARG cc_start: 0.7009 (ptp-110) cc_final: 0.6576 (mtm-85) REVERT: A 270 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8905 (p0) REVERT: A 332 MET cc_start: 0.8618 (tpp) cc_final: 0.8165 (tpp) REVERT: B 115 HIS cc_start: 0.5718 (OUTLIER) cc_final: 0.5468 (t70) REVERT: B 351 ASN cc_start: 0.7551 (p0) cc_final: 0.7245 (p0) REVERT: C 115 HIS cc_start: 0.5453 (OUTLIER) cc_final: 0.5148 (t70) REVERT: C 239 ARG cc_start: 0.7223 (ptp-110) cc_final: 0.6880 (mtm180) REVERT: C 473 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7600 (mm-40) REVERT: D 84 MET cc_start: 0.6016 (ppp) cc_final: 0.5802 (tmm) REVERT: D 115 HIS cc_start: 0.5965 (OUTLIER) cc_final: 0.5671 (t70) REVERT: D 239 ARG cc_start: 0.7025 (ptp-110) cc_final: 0.6695 (mtm-85) REVERT: D 270 ASN cc_start: 0.9085 (OUTLIER) cc_final: 0.8863 (p0) REVERT: E 115 HIS cc_start: 0.5705 (OUTLIER) cc_final: 0.5476 (t70) REVERT: F 115 HIS cc_start: 0.5592 (OUTLIER) cc_final: 0.5317 (t70) REVERT: F 239 ARG cc_start: 0.7175 (ptp-110) cc_final: 0.6779 (mtm180) REVERT: F 473 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7589 (mm-40) outliers start: 104 outliers final: 79 residues processed: 420 average time/residue: 0.5117 time to fit residues: 353.0668 Evaluate side-chains 407 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 320 time to evaluate : 3.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 732 ARG Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 732 ARG Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 732 ARG Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.5980 chunk 243 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 319 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 366 optimal weight: 20.0000 chunk 296 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 219 optimal weight: 30.0000 chunk 385 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35772 Z= 0.251 Angle : 0.625 12.602 48354 Z= 0.297 Chirality : 0.046 0.174 5418 Planarity : 0.004 0.058 6372 Dihedral : 9.474 137.808 4968 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.28 % Allowed : 16.32 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.09 (0.13), residues: 4416 helix: 0.29 (0.13), residues: 1800 sheet: -0.76 (0.19), residues: 714 loop : -1.67 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 454 HIS 0.003 0.001 HIS B 115 PHE 0.013 0.001 PHE F 363 TYR 0.021 0.002 TYR F 244 ARG 0.005 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 338 time to evaluate : 4.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.5921 (OUTLIER) cc_final: 0.5697 (t70) REVERT: A 239 ARG cc_start: 0.7026 (ptp-110) cc_final: 0.6592 (mtm-85) REVERT: A 270 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8903 (p0) REVERT: A 332 MET cc_start: 0.8686 (tpp) cc_final: 0.8248 (tpp) REVERT: B 115 HIS cc_start: 0.5849 (OUTLIER) cc_final: 0.5501 (t70) REVERT: B 351 ASN cc_start: 0.7626 (p0) cc_final: 0.7320 (p0) REVERT: C 115 HIS cc_start: 0.5565 (OUTLIER) cc_final: 0.5351 (t70) REVERT: C 239 ARG cc_start: 0.7301 (ptp-110) cc_final: 0.6906 (mtm180) REVERT: C 473 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7604 (mm-40) REVERT: D 115 HIS cc_start: 0.5878 (OUTLIER) cc_final: 0.5675 (t70) REVERT: D 239 ARG cc_start: 0.7017 (ptp-110) cc_final: 0.6686 (mtm-85) REVERT: D 270 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8899 (p0) REVERT: E 115 HIS cc_start: 0.5732 (OUTLIER) cc_final: 0.5527 (t70) REVERT: F 115 HIS cc_start: 0.5547 (OUTLIER) cc_final: 0.5335 (t70) REVERT: F 239 ARG cc_start: 0.7150 (ptp-110) cc_final: 0.6743 (mtm180) outliers start: 124 outliers final: 94 residues processed: 436 average time/residue: 0.4632 time to fit residues: 329.4683 Evaluate side-chains 421 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 319 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 732 ARG Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 732 ARG Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 732 ARG Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 20.0000 chunk 386 optimal weight: 0.2980 chunk 84 optimal weight: 0.0070 chunk 251 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 429 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 225 optimal weight: 30.0000 overall best weight: 2.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 215 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35772 Z= 0.179 Angle : 0.601 13.226 48354 Z= 0.282 Chirality : 0.045 0.228 5418 Planarity : 0.004 0.057 6372 Dihedral : 8.987 140.649 4968 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.88 % Allowed : 17.33 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.13), residues: 4416 helix: 0.51 (0.13), residues: 1794 sheet: -0.58 (0.19), residues: 714 loop : -1.59 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 454 HIS 0.002 0.001 HIS B 115 PHE 0.012 0.001 PHE F 363 TYR 0.016 0.001 TYR F 244 ARG 0.008 0.000 ARG F 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 353 time to evaluate : 4.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.5942 (OUTLIER) cc_final: 0.5740 (t70) REVERT: A 239 ARG cc_start: 0.7002 (ptp-110) cc_final: 0.6560 (mtm-85) REVERT: A 270 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8685 (p0) REVERT: A 332 MET cc_start: 0.8678 (tpp) cc_final: 0.8203 (tpp) REVERT: B 115 HIS cc_start: 0.5630 (OUTLIER) cc_final: 0.5374 (t70) REVERT: B 327 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8158 (tp-100) REVERT: B 351 ASN cc_start: 0.7657 (p0) cc_final: 0.7352 (p0) REVERT: C 239 ARG cc_start: 0.7216 (ptp-110) cc_final: 0.6855 (mtm180) REVERT: C 327 GLN cc_start: 0.8446 (tp-100) cc_final: 0.7972 (tp-100) REVERT: D 239 ARG cc_start: 0.7018 (ptp-110) cc_final: 0.6585 (mtm-85) REVERT: D 270 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8652 (p0) REVERT: D 473 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7404 (mm-40) REVERT: E 327 GLN cc_start: 0.8473 (tp-100) cc_final: 0.8102 (tp-100) REVERT: F 239 ARG cc_start: 0.7234 (ptp-110) cc_final: 0.6860 (mtm180) REVERT: F 327 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8043 (tp-100) outliers start: 109 outliers final: 78 residues processed: 428 average time/residue: 0.4623 time to fit residues: 323.3233 Evaluate side-chains 410 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 328 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 732 ARG Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 732 ARG Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 361 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 427 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS C 602 ASN D 215 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35772 Z= 0.294 Angle : 0.653 13.022 48354 Z= 0.309 Chirality : 0.046 0.186 5418 Planarity : 0.004 0.058 6372 Dihedral : 8.819 142.982 4968 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.35 % Allowed : 17.83 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.90 (0.13), residues: 4416 helix: 0.40 (0.13), residues: 1800 sheet: -0.44 (0.20), residues: 660 loop : -1.59 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 476 HIS 0.004 0.001 HIS E 735 PHE 0.013 0.001 PHE C 363 TYR 0.021 0.002 TYR F 244 ARG 0.014 0.001 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 321 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.7063 (ptp-110) cc_final: 0.6537 (mtm-85) REVERT: A 270 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8738 (p0) REVERT: A 332 MET cc_start: 0.8691 (tpp) cc_final: 0.8174 (tpp) REVERT: B 115 HIS cc_start: 0.5856 (OUTLIER) cc_final: 0.5543 (t70) REVERT: C 25 ARG cc_start: 0.6009 (mmm-85) cc_final: 0.5806 (mmm-85) REVERT: C 239 ARG cc_start: 0.7305 (ptp-110) cc_final: 0.6881 (mtm180) REVERT: C 611 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6965 (ttm) REVERT: D 239 ARG cc_start: 0.7038 (ptp-110) cc_final: 0.6600 (mtm-85) REVERT: D 270 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8700 (p0) REVERT: D 473 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7399 (mm-40) REVERT: F 239 ARG cc_start: 0.7273 (ptp-110) cc_final: 0.6878 (mtm180) REVERT: F 611 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6947 (ttm) outliers start: 127 outliers final: 106 residues processed: 419 average time/residue: 0.4975 time to fit residues: 338.9716 Evaluate side-chains 420 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 309 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 732 ARG Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 732 ARG Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 30.0000 chunk 170 optimal weight: 0.1980 chunk 255 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 82 optimal weight: 30.0000 chunk 272 optimal weight: 0.0270 chunk 291 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 336 optimal weight: 7.9990 overall best weight: 1.2620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN E 33 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35772 Z= 0.160 Angle : 0.601 12.768 48354 Z= 0.281 Chirality : 0.044 0.164 5418 Planarity : 0.004 0.058 6372 Dihedral : 8.432 141.004 4968 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.27 % Allowed : 19.02 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.60 (0.13), residues: 4416 helix: 0.70 (0.13), residues: 1794 sheet: -0.26 (0.20), residues: 666 loop : -1.48 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 454 HIS 0.003 0.001 HIS A 115 PHE 0.013 0.001 PHE C 363 TYR 0.019 0.001 TYR F 138 ARG 0.008 0.000 ARG D 753 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 352 time to evaluate : 4.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.6970 (ptp-110) cc_final: 0.6476 (mtm-85) REVERT: A 270 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8595 (p0) REVERT: A 332 MET cc_start: 0.8676 (tpp) cc_final: 0.8123 (tpp) REVERT: B 115 HIS cc_start: 0.5684 (OUTLIER) cc_final: 0.5478 (t70) REVERT: B 327 GLN cc_start: 0.8435 (tp-100) cc_final: 0.8100 (tp-100) REVERT: B 351 ASN cc_start: 0.7782 (p0) cc_final: 0.7482 (p0) REVERT: C 239 ARG cc_start: 0.7175 (ptp-110) cc_final: 0.6763 (mtm180) REVERT: C 327 GLN cc_start: 0.8426 (tp-100) cc_final: 0.7987 (tp-100) REVERT: C 611 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6947 (ttm) REVERT: C 616 ASN cc_start: 0.7955 (t0) cc_final: 0.7705 (t0) REVERT: D 239 ARG cc_start: 0.7021 (ptp-110) cc_final: 0.6613 (mtm-85) REVERT: D 270 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8607 (p0) REVERT: D 473 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7369 (mm-40) REVERT: E 327 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8111 (tp-100) REVERT: F 239 ARG cc_start: 0.7237 (ptp-110) cc_final: 0.6848 (mtm180) REVERT: F 327 GLN cc_start: 0.8473 (tp-100) cc_final: 0.8016 (tp-100) REVERT: F 611 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6984 (ttm) outliers start: 86 outliers final: 75 residues processed: 413 average time/residue: 0.4726 time to fit residues: 318.1709 Evaluate side-chains 404 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 324 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 4.9990 chunk 409 optimal weight: 9.9990 chunk 374 optimal weight: 3.9990 chunk 398 optimal weight: 9.9990 chunk 240 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 313 optimal weight: 40.0000 chunk 122 optimal weight: 7.9990 chunk 360 optimal weight: 0.0020 chunk 377 optimal weight: 9.9990 chunk 397 optimal weight: 5.9990 overall best weight: 3.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS A 750 ASN B 33 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN D 735 HIS E 33 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35772 Z= 0.208 Angle : 0.623 13.725 48354 Z= 0.291 Chirality : 0.045 0.165 5418 Planarity : 0.004 0.058 6372 Dihedral : 8.394 140.440 4968 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.72 % Allowed : 19.23 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.56 (0.13), residues: 4416 helix: 0.73 (0.13), residues: 1794 sheet: -0.23 (0.20), residues: 666 loop : -1.47 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 454 HIS 0.002 0.001 HIS A 183 PHE 0.020 0.001 PHE C 363 TYR 0.022 0.002 TYR C 138 ARG 0.008 0.000 ARG D 753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 331 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.7005 (ptp-110) cc_final: 0.6593 (mtm-85) REVERT: A 270 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8644 (p0) REVERT: A 332 MET cc_start: 0.8666 (tpp) cc_final: 0.8140 (tpp) REVERT: B 115 HIS cc_start: 0.5728 (OUTLIER) cc_final: 0.5510 (t70) REVERT: C 239 ARG cc_start: 0.7253 (ptp-110) cc_final: 0.6879 (mtm180) REVERT: C 327 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8050 (tp-100) REVERT: C 473 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7296 (mm-40) REVERT: C 611 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6892 (ttm) REVERT: C 616 ASN cc_start: 0.7962 (t0) cc_final: 0.7679 (t0) REVERT: D 239 ARG cc_start: 0.7079 (ptp-110) cc_final: 0.6640 (mtm-85) REVERT: D 270 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8668 (p0) REVERT: D 473 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7397 (mm-40) REVERT: F 239 ARG cc_start: 0.7183 (ptp-110) cc_final: 0.6891 (mtm180) REVERT: F 327 GLN cc_start: 0.8489 (tp-100) cc_final: 0.8029 (tp-100) REVERT: F 388 MET cc_start: 0.7493 (mtp) cc_final: 0.7214 (mtp) REVERT: F 611 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6992 (ttm) outliers start: 103 outliers final: 90 residues processed: 407 average time/residue: 0.4620 time to fit residues: 312.2096 Evaluate side-chains 418 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 323 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 3.9990 chunk 421 optimal weight: 8.9990 chunk 257 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 293 optimal weight: 9.9990 chunk 442 optimal weight: 1.9990 chunk 407 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 272 optimal weight: 0.0010 chunk 215 optimal weight: 7.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35772 Z= 0.166 Angle : 0.619 13.452 48354 Z= 0.287 Chirality : 0.044 0.159 5418 Planarity : 0.004 0.058 6372 Dihedral : 8.298 139.219 4968 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.69 % Allowed : 19.52 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.44 (0.13), residues: 4416 helix: 0.84 (0.13), residues: 1794 sheet: -0.14 (0.20), residues: 666 loop : -1.41 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 454 HIS 0.002 0.001 HIS A 183 PHE 0.010 0.001 PHE F 363 TYR 0.019 0.001 TYR C 138 ARG 0.007 0.000 ARG A 753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 330 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.6988 (ptp-110) cc_final: 0.6505 (mtm-85) REVERT: A 270 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8562 (p0) REVERT: A 327 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8392 (tm-30) REVERT: A 332 MET cc_start: 0.8662 (tpp) cc_final: 0.8133 (tpp) REVERT: B 327 GLN cc_start: 0.8433 (tp-100) cc_final: 0.8115 (tp-100) REVERT: C 239 ARG cc_start: 0.7128 (ptp-110) cc_final: 0.6828 (mtm180) REVERT: C 327 GLN cc_start: 0.8479 (tp-100) cc_final: 0.7961 (tp-100) REVERT: C 473 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7173 (mm-40) REVERT: C 611 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6981 (ttm) REVERT: C 616 ASN cc_start: 0.7869 (t0) cc_final: 0.7584 (t0) REVERT: D 239 ARG cc_start: 0.7024 (ptp-110) cc_final: 0.6619 (mtm-85) REVERT: D 270 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8594 (p0) REVERT: D 473 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7395 (mm-40) REVERT: E 327 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8137 (tp-100) REVERT: F 239 ARG cc_start: 0.7159 (ptp-110) cc_final: 0.6858 (mtm180) REVERT: F 327 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8020 (tp-100) REVERT: F 388 MET cc_start: 0.7484 (mtp) cc_final: 0.7269 (mtp) REVERT: F 611 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7021 (ttm) REVERT: F 616 ASN cc_start: 0.7862 (t0) cc_final: 0.7599 (t0) outliers start: 102 outliers final: 87 residues processed: 405 average time/residue: 0.4445 time to fit residues: 297.7003 Evaluate side-chains 412 residues out of total 3786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 321 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 732 ARG Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 10.0000 chunk 375 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 324 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 352 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 362 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN B 33 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106599 restraints weight = 65236.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105279 restraints weight = 81860.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106582 restraints weight = 83078.080| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35772 Z= 0.249 Angle : 0.640 13.531 48354 Z= 0.299 Chirality : 0.045 0.161 5418 Planarity : 0.004 0.058 6372 Dihedral : 8.400 139.499 4968 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.72 % Allowed : 19.60 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.54 (0.13), residues: 4416 helix: 0.69 (0.13), residues: 1806 sheet: -0.16 (0.20), residues: 666 loop : -1.43 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 476 HIS 0.002 0.001 HIS D 404 PHE 0.014 0.001 PHE F 363 TYR 0.027 0.002 TYR E 244 ARG 0.007 0.000 ARG E 635 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6647.27 seconds wall clock time: 121 minutes 55.23 seconds (7315.23 seconds total)