Starting phenix.real_space_refine on Mon Mar 25 10:39:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz4_25560/03_2024/7sz4_25560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz4_25560/03_2024/7sz4_25560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz4_25560/03_2024/7sz4_25560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz4_25560/03_2024/7sz4_25560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz4_25560/03_2024/7sz4_25560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sz4_25560/03_2024/7sz4_25560.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 285 5.16 5 C 30322 2.51 5 N 8431 2.21 5 O 9204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "k PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 349": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48242 Number of models: 1 Model: "" Number of chains: 12 Chain: "k" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4074 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 15, 'TRANS': 489} Chain breaks: 3 Chain: "j" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4074 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 15, 'TRANS': 489} Chain breaks: 3 Chain: "i" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3820 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 14, 'TRANS': 456} Chain breaks: 4 Chain: "h" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3791 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 4 Chain: "l" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4074 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 15, 'TRANS': 489} Chain breaks: 3 Chain: "a" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4074 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 15, 'TRANS': 489} Chain breaks: 3 Chain: "b" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4074 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 15, 'TRANS': 489} Chain breaks: 3 Chain: "c" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4074 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 15, 'TRANS': 489} Chain breaks: 3 Chain: "d" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4074 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 15, 'TRANS': 489} Chain breaks: 3 Chain: "e" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4074 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 15, 'TRANS': 489} Chain breaks: 3 Chain: "f" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4074 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 15, 'TRANS': 489} Chain breaks: 3 Chain: "g" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3965 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 15, 'TRANS': 474} Chain breaks: 5 Time building chain proxies: 23.44, per 1000 atoms: 0.49 Number of scatterers: 48242 At special positions: 0 Unit cell: (196.56, 194.74, 147.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 285 16.00 O 9204 8.00 N 8431 7.00 C 30322 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: 18.96 Conformation dependent library (CDL) restraints added in 8.1 seconds 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11214 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 33 sheets defined 49.1% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'k' and resid 13 through 46 Processing helix chain 'k' and resid 64 through 81 removed outlier: 3.615A pdb=" N THR k 68 " --> pdb=" O ASP k 64 " (cutoff:3.500A) Proline residue: k 74 - end of helix Processing helix chain 'k' and resid 99 through 115 removed outlier: 4.461A pdb=" N ARG k 113 " --> pdb=" O TYR k 109 " (cutoff:3.500A) Processing helix chain 'k' and resid 118 through 131 Processing helix chain 'k' and resid 200 through 204 removed outlier: 3.526A pdb=" N PHE k 204 " --> pdb=" O PRO k 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 212 through 216 removed outlier: 3.573A pdb=" N ASP k 215 " --> pdb=" O CYS k 212 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA k 216 " --> pdb=" O ILE k 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 212 through 216' Processing helix chain 'k' and resid 226 through 234 Processing helix chain 'k' and resid 339 through 368 removed outlier: 3.706A pdb=" N LYS k 343 " --> pdb=" O SER k 339 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASP k 346 " --> pdb=" O ASP k 342 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE k 347 " --> pdb=" O LYS k 343 " (cutoff:3.500A) Processing helix chain 'k' and resid 379 through 385 Processing helix chain 'k' and resid 408 through 410 No H-bonds generated for 'chain 'k' and resid 408 through 410' Processing helix chain 'k' and resid 411 through 426 removed outlier: 4.018A pdb=" N LEU k 415 " --> pdb=" O VAL k 411 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP k 416 " --> pdb=" O TYR k 412 " (cutoff:3.500A) Processing helix chain 'k' and resid 448 through 458 Processing helix chain 'k' and resid 459 through 485 removed outlier: 3.555A pdb=" N ILE k 463 " --> pdb=" O GLN k 459 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS k 473 " --> pdb=" O GLU k 469 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG k 474 " --> pdb=" O THR k 470 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS k 485 " --> pdb=" O ASP k 481 " (cutoff:3.500A) Processing helix chain 'k' and resid 522 through 545 Processing helix chain 'k' and resid 552 through 568 removed outlier: 4.431A pdb=" N ASN k 558 " --> pdb=" O GLN k 554 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL k 563 " --> pdb=" O ILE k 559 " (cutoff:3.500A) Processing helix chain 'k' and resid 581 through 588 Processing helix chain 'j' and resid 13 through 46 Processing helix chain 'j' and resid 64 through 81 removed outlier: 3.566A pdb=" N THR j 68 " --> pdb=" O ASP j 64 " (cutoff:3.500A) Proline residue: j 74 - end of helix Processing helix chain 'j' and resid 99 through 115 removed outlier: 4.467A pdb=" N ARG j 113 " --> pdb=" O TYR j 109 " (cutoff:3.500A) Processing helix chain 'j' and resid 118 through 131 Processing helix chain 'j' and resid 200 through 204 removed outlier: 3.614A pdb=" N PHE j 204 " --> pdb=" O PRO j 201 " (cutoff:3.500A) Processing helix chain 'j' and resid 212 through 216 removed outlier: 3.600A pdb=" N ASP j 215 " --> pdb=" O CYS j 212 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA j 216 " --> pdb=" O ILE j 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 212 through 216' Processing helix chain 'j' and resid 226 through 234 Processing helix chain 'j' and resid 339 through 368 removed outlier: 3.570A pdb=" N LYS j 343 " --> pdb=" O SER j 339 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP j 346 " --> pdb=" O ASP j 342 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE j 347 " --> pdb=" O LYS j 343 " (cutoff:3.500A) Processing helix chain 'j' and resid 379 through 385 removed outlier: 3.584A pdb=" N ASN j 385 " --> pdb=" O LEU j 382 " (cutoff:3.500A) Processing helix chain 'j' and resid 409 through 426 removed outlier: 3.710A pdb=" N GLY j 413 " --> pdb=" O GLY j 409 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET j 414 " --> pdb=" O GLU j 410 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU j 415 " --> pdb=" O VAL j 411 " (cutoff:3.500A) Processing helix chain 'j' and resid 448 through 458 Processing helix chain 'j' and resid 459 through 484 removed outlier: 4.160A pdb=" N LYS j 473 " --> pdb=" O GLU j 469 " (cutoff:3.500A) Processing helix chain 'j' and resid 522 through 545 removed outlier: 4.025A pdb=" N GLN j 526 " --> pdb=" O MET j 522 " (cutoff:3.500A) Processing helix chain 'j' and resid 552 through 568 removed outlier: 4.638A pdb=" N ASN j 558 " --> pdb=" O GLN j 554 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL j 563 " --> pdb=" O ILE j 559 " (cutoff:3.500A) Processing helix chain 'j' and resid 581 through 588 removed outlier: 3.612A pdb=" N GLN j 586 " --> pdb=" O PRO j 582 " (cutoff:3.500A) Processing helix chain 'i' and resid 13 through 46 Processing helix chain 'i' and resid 64 through 81 removed outlier: 3.575A pdb=" N THR i 68 " --> pdb=" O ASP i 64 " (cutoff:3.500A) Proline residue: i 74 - end of helix Processing helix chain 'i' and resid 99 through 115 removed outlier: 4.437A pdb=" N ARG i 113 " --> pdb=" O TYR i 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 118 through 131 Processing helix chain 'i' and resid 200 through 204 removed outlier: 3.667A pdb=" N PHE i 204 " --> pdb=" O PRO i 201 " (cutoff:3.500A) Processing helix chain 'i' and resid 212 through 216 removed outlier: 3.595A pdb=" N ASP i 215 " --> pdb=" O CYS i 212 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA i 216 " --> pdb=" O ILE i 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 212 through 216' Processing helix chain 'i' and resid 226 through 234 Processing helix chain 'i' and resid 339 through 368 removed outlier: 3.552A pdb=" N LYS i 343 " --> pdb=" O SER i 339 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASP i 346 " --> pdb=" O ASP i 342 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILE i 347 " --> pdb=" O LYS i 343 " (cutoff:3.500A) Processing helix chain 'i' and resid 409 through 426 removed outlier: 3.501A pdb=" N GLY i 413 " --> pdb=" O GLY i 409 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG i 417 " --> pdb=" O GLY i 413 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU i 419 " --> pdb=" O LEU i 415 " (cutoff:3.500A) Processing helix chain 'i' and resid 448 through 458 Processing helix chain 'i' and resid 459 through 484 Processing helix chain 'i' and resid 522 through 545 removed outlier: 3.685A pdb=" N GLN i 526 " --> pdb=" O MET i 522 " (cutoff:3.500A) Processing helix chain 'i' and resid 552 through 567 removed outlier: 4.500A pdb=" N ASN i 558 " --> pdb=" O GLN i 554 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL i 563 " --> pdb=" O ILE i 559 " (cutoff:3.500A) Processing helix chain 'i' and resid 581 through 588 removed outlier: 3.632A pdb=" N GLN i 586 " --> pdb=" O PRO i 582 " (cutoff:3.500A) Processing helix chain 'i' and resid 590 through 595 Processing helix chain 'h' and resid 13 through 47 removed outlier: 3.665A pdb=" N ARG h 17 " --> pdb=" O GLU h 13 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 81 Proline residue: h 74 - end of helix Processing helix chain 'h' and resid 99 through 115 removed outlier: 3.822A pdb=" N MET h 112 " --> pdb=" O ASN h 108 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG h 113 " --> pdb=" O TYR h 109 " (cutoff:3.500A) Processing helix chain 'h' and resid 118 through 130 Processing helix chain 'h' and resid 200 through 204 removed outlier: 3.757A pdb=" N PHE h 204 " --> pdb=" O PRO h 201 " (cutoff:3.500A) Processing helix chain 'h' and resid 212 through 216 removed outlier: 3.592A pdb=" N ASP h 215 " --> pdb=" O CYS h 212 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA h 216 " --> pdb=" O ILE h 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 212 through 216' Processing helix chain 'h' and resid 226 through 234 Processing helix chain 'h' and resid 339 through 366 removed outlier: 5.641A pdb=" N ASP h 346 " --> pdb=" O ASP h 342 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE h 347 " --> pdb=" O LYS h 343 " (cutoff:3.500A) Processing helix chain 'h' and resid 409 through 426 removed outlier: 3.966A pdb=" N ARG h 417 " --> pdb=" O GLY h 413 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG h 425 " --> pdb=" O ASP h 421 " (cutoff:3.500A) Processing helix chain 'h' and resid 448 through 458 Processing helix chain 'h' and resid 459 through 484 Processing helix chain 'h' and resid 522 through 545 removed outlier: 3.668A pdb=" N GLN h 526 " --> pdb=" O MET h 522 " (cutoff:3.500A) Processing helix chain 'h' and resid 552 through 568 removed outlier: 4.130A pdb=" N ASN h 558 " --> pdb=" O GLN h 554 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL h 563 " --> pdb=" O ILE h 559 " (cutoff:3.500A) Processing helix chain 'h' and resid 581 through 588 removed outlier: 3.582A pdb=" N GLN h 586 " --> pdb=" O PRO h 582 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 46 Processing helix chain 'l' and resid 64 through 81 removed outlier: 3.626A pdb=" N THR l 68 " --> pdb=" O ASP l 64 " (cutoff:3.500A) Proline residue: l 74 - end of helix Processing helix chain 'l' and resid 99 through 115 removed outlier: 4.417A pdb=" N ARG l 113 " --> pdb=" O TYR l 109 " (cutoff:3.500A) Processing helix chain 'l' and resid 118 through 130 Processing helix chain 'l' and resid 200 through 204 removed outlier: 3.708A pdb=" N PHE l 204 " --> pdb=" O PRO l 201 " (cutoff:3.500A) Processing helix chain 'l' and resid 212 through 216 removed outlier: 3.788A pdb=" N ALA l 216 " --> pdb=" O ILE l 213 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 234 Processing helix chain 'l' and resid 339 through 368 removed outlier: 6.216A pdb=" N ASP l 346 " --> pdb=" O ASP l 342 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE l 347 " --> pdb=" O LYS l 343 " (cutoff:3.500A) Processing helix chain 'l' and resid 379 through 385 Processing helix chain 'l' and resid 409 through 426 removed outlier: 3.751A pdb=" N GLY l 413 " --> pdb=" O GLY l 409 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU l 419 " --> pdb=" O LEU l 415 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 458 Processing helix chain 'l' and resid 459 through 484 removed outlier: 3.589A pdb=" N PHE l 467 " --> pdb=" O ILE l 463 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA l 468 " --> pdb=" O ALA l 464 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS l 473 " --> pdb=" O GLU l 469 " (cutoff:3.500A) Processing helix chain 'l' and resid 512 through 516 removed outlier: 4.031A pdb=" N VAL l 515 " --> pdb=" O ASP l 512 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR l 516 " --> pdb=" O LEU l 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 512 through 516' Processing helix chain 'l' and resid 522 through 545 removed outlier: 3.834A pdb=" N GLN l 526 " --> pdb=" O MET l 522 " (cutoff:3.500A) Processing helix chain 'l' and resid 552 through 568 removed outlier: 4.715A pdb=" N ASN l 558 " --> pdb=" O GLN l 554 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL l 563 " --> pdb=" O ILE l 559 " (cutoff:3.500A) Processing helix chain 'l' and resid 581 through 589 removed outlier: 3.652A pdb=" N GLN l 586 " --> pdb=" O PRO l 582 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 46 Processing helix chain 'a' and resid 64 through 81 removed outlier: 3.812A pdb=" N THR a 68 " --> pdb=" O ASP a 64 " (cutoff:3.500A) Proline residue: a 74 - end of helix Processing helix chain 'a' and resid 99 through 115 removed outlier: 4.507A pdb=" N ARG a 113 " --> pdb=" O TYR a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 118 through 131 Processing helix chain 'a' and resid 200 through 204 removed outlier: 3.784A pdb=" N PHE a 204 " --> pdb=" O PRO a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.838A pdb=" N ALA a 216 " --> pdb=" O ILE a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 226 through 234 Processing helix chain 'a' and resid 339 through 368 removed outlier: 6.329A pdb=" N ASP a 346 " --> pdb=" O ASP a 342 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ILE a 347 " --> pdb=" O LYS a 343 " (cutoff:3.500A) Processing helix chain 'a' and resid 379 through 385 Processing helix chain 'a' and resid 408 through 410 No H-bonds generated for 'chain 'a' and resid 408 through 410' Processing helix chain 'a' and resid 411 through 426 removed outlier: 4.138A pdb=" N LEU a 415 " --> pdb=" O VAL a 411 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP a 416 " --> pdb=" O TYR a 412 " (cutoff:3.500A) Processing helix chain 'a' and resid 448 through 458 Processing helix chain 'a' and resid 459 through 484 removed outlier: 4.164A pdb=" N LYS a 473 " --> pdb=" O GLU a 469 " (cutoff:3.500A) Processing helix chain 'a' and resid 512 through 516 removed outlier: 3.748A pdb=" N VAL a 515 " --> pdb=" O ASP a 512 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR a 516 " --> pdb=" O LEU a 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 512 through 516' Processing helix chain 'a' and resid 522 through 544 Processing helix chain 'a' and resid 552 through 568 removed outlier: 4.647A pdb=" N ASN a 558 " --> pdb=" O GLN a 554 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL a 563 " --> pdb=" O ILE a 559 " (cutoff:3.500A) Processing helix chain 'a' and resid 581 through 589 removed outlier: 3.505A pdb=" N GLN a 586 " --> pdb=" O PRO a 582 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 46 Processing helix chain 'b' and resid 64 through 81 removed outlier: 3.765A pdb=" N THR b 68 " --> pdb=" O ASP b 64 " (cutoff:3.500A) Proline residue: b 74 - end of helix Processing helix chain 'b' and resid 99 through 115 removed outlier: 4.438A pdb=" N ARG b 113 " --> pdb=" O TYR b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 130 removed outlier: 3.524A pdb=" N TRP b 124 " --> pdb=" O VAL b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 200 through 204 Processing helix chain 'b' and resid 212 through 216 removed outlier: 3.634A pdb=" N ASP b 215 " --> pdb=" O CYS b 212 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA b 216 " --> pdb=" O ILE b 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 212 through 216' Processing helix chain 'b' and resid 226 through 234 Processing helix chain 'b' and resid 339 through 368 removed outlier: 6.077A pdb=" N ASP b 346 " --> pdb=" O ASP b 342 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE b 347 " --> pdb=" O LYS b 343 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 Processing helix chain 'b' and resid 409 through 426 removed outlier: 3.606A pdb=" N GLY b 413 " --> pdb=" O GLY b 409 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET b 414 " --> pdb=" O GLU b 410 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU b 415 " --> pdb=" O VAL b 411 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP b 416 " --> pdb=" O TYR b 412 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG b 417 " --> pdb=" O GLY b 413 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU b 419 " --> pdb=" O LEU b 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 458 Processing helix chain 'b' and resid 459 through 485 removed outlier: 4.014A pdb=" N LYS b 473 " --> pdb=" O GLU b 469 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG b 474 " --> pdb=" O THR b 470 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS b 485 " --> pdb=" O ASP b 481 " (cutoff:3.500A) Processing helix chain 'b' and resid 512 through 516 removed outlier: 3.994A pdb=" N VAL b 515 " --> pdb=" O ASP b 512 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR b 516 " --> pdb=" O LEU b 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 512 through 516' Processing helix chain 'b' and resid 522 through 545 Processing helix chain 'b' and resid 552 through 567 removed outlier: 4.611A pdb=" N ASN b 558 " --> pdb=" O GLN b 554 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL b 563 " --> pdb=" O ILE b 559 " (cutoff:3.500A) Processing helix chain 'b' and resid 581 through 588 Processing helix chain 'c' and resid 13 through 46 Processing helix chain 'c' and resid 64 through 81 removed outlier: 4.060A pdb=" N THR c 68 " --> pdb=" O ASP c 64 " (cutoff:3.500A) Proline residue: c 74 - end of helix Processing helix chain 'c' and resid 99 through 115 removed outlier: 4.519A pdb=" N ARG c 113 " --> pdb=" O TYR c 109 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 131 Processing helix chain 'c' and resid 200 through 204 removed outlier: 3.511A pdb=" N PHE c 204 " --> pdb=" O PRO c 201 " (cutoff:3.500A) Processing helix chain 'c' and resid 212 through 216 removed outlier: 3.548A pdb=" N ASP c 215 " --> pdb=" O CYS c 212 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA c 216 " --> pdb=" O ILE c 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 212 through 216' Processing helix chain 'c' and resid 226 through 234 Processing helix chain 'c' and resid 339 through 368 removed outlier: 6.324A pdb=" N ASP c 346 " --> pdb=" O ASP c 342 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE c 347 " --> pdb=" O LYS c 343 " (cutoff:3.500A) Processing helix chain 'c' and resid 379 through 385 Processing helix chain 'c' and resid 410 through 426 removed outlier: 3.504A pdb=" N MET c 414 " --> pdb=" O GLU c 410 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG c 417 " --> pdb=" O GLY c 413 " (cutoff:3.500A) Processing helix chain 'c' and resid 448 through 458 Processing helix chain 'c' and resid 459 through 485 removed outlier: 3.999A pdb=" N LYS c 473 " --> pdb=" O GLU c 469 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG c 474 " --> pdb=" O THR c 470 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS c 485 " --> pdb=" O ASP c 481 " (cutoff:3.500A) Processing helix chain 'c' and resid 512 through 516 removed outlier: 3.780A pdb=" N VAL c 515 " --> pdb=" O ASP c 512 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR c 516 " --> pdb=" O LEU c 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 512 through 516' Processing helix chain 'c' and resid 522 through 545 Processing helix chain 'c' and resid 552 through 568 removed outlier: 4.614A pdb=" N ASN c 558 " --> pdb=" O GLN c 554 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL c 563 " --> pdb=" O ILE c 559 " (cutoff:3.500A) Processing helix chain 'c' and resid 581 through 589 Processing helix chain 'd' and resid 13 through 46 Processing helix chain 'd' and resid 64 through 81 removed outlier: 3.882A pdb=" N THR d 68 " --> pdb=" O ASP d 64 " (cutoff:3.500A) Proline residue: d 74 - end of helix Processing helix chain 'd' and resid 99 through 115 removed outlier: 4.441A pdb=" N ARG d 113 " --> pdb=" O TYR d 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 131 Processing helix chain 'd' and resid 200 through 204 removed outlier: 3.675A pdb=" N PHE d 204 " --> pdb=" O PRO d 201 " (cutoff:3.500A) Processing helix chain 'd' and resid 212 through 216 removed outlier: 3.724A pdb=" N ASP d 215 " --> pdb=" O CYS d 212 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA d 216 " --> pdb=" O ILE d 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 212 through 216' Processing helix chain 'd' and resid 226 through 234 Processing helix chain 'd' and resid 339 through 368 removed outlier: 6.322A pdb=" N ASP d 346 " --> pdb=" O ASP d 342 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE d 347 " --> pdb=" O LYS d 343 " (cutoff:3.500A) Processing helix chain 'd' and resid 379 through 385 removed outlier: 3.538A pdb=" N ASN d 385 " --> pdb=" O LEU d 382 " (cutoff:3.500A) Processing helix chain 'd' and resid 410 through 426 removed outlier: 3.768A pdb=" N MET d 414 " --> pdb=" O GLU d 410 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU d 415 " --> pdb=" O VAL d 411 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 Processing helix chain 'd' and resid 459 through 485 removed outlier: 3.932A pdb=" N LYS d 473 " --> pdb=" O GLU d 469 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG d 474 " --> pdb=" O THR d 470 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS d 485 " --> pdb=" O ASP d 481 " (cutoff:3.500A) Processing helix chain 'd' and resid 522 through 545 Processing helix chain 'd' and resid 552 through 568 removed outlier: 4.539A pdb=" N ASN d 558 " --> pdb=" O GLN d 554 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL d 563 " --> pdb=" O ILE d 559 " (cutoff:3.500A) Processing helix chain 'd' and resid 581 through 589 Processing helix chain 'e' and resid 13 through 47 Processing helix chain 'e' and resid 64 through 81 removed outlier: 3.907A pdb=" N THR e 68 " --> pdb=" O ASP e 64 " (cutoff:3.500A) Proline residue: e 74 - end of helix Processing helix chain 'e' and resid 99 through 115 removed outlier: 4.091A pdb=" N MET e 112 " --> pdb=" O ASN e 108 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG e 113 " --> pdb=" O TYR e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 130 Processing helix chain 'e' and resid 200 through 204 Processing helix chain 'e' and resid 212 through 216 removed outlier: 3.890A pdb=" N ALA e 216 " --> pdb=" O ILE e 213 " (cutoff:3.500A) Processing helix chain 'e' and resid 226 through 234 Processing helix chain 'e' and resid 339 through 368 removed outlier: 6.272A pdb=" N ASP e 346 " --> pdb=" O ASP e 342 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE e 347 " --> pdb=" O LYS e 343 " (cutoff:3.500A) Processing helix chain 'e' and resid 379 through 385 removed outlier: 3.571A pdb=" N ASN e 385 " --> pdb=" O LEU e 382 " (cutoff:3.500A) Processing helix chain 'e' and resid 409 through 426 removed outlier: 3.830A pdb=" N GLY e 413 " --> pdb=" O GLY e 409 " (cutoff:3.500A) Processing helix chain 'e' and resid 448 through 458 Processing helix chain 'e' and resid 459 through 485 removed outlier: 4.030A pdb=" N LYS e 473 " --> pdb=" O GLU e 469 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG e 474 " --> pdb=" O THR e 470 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS e 485 " --> pdb=" O ASP e 481 " (cutoff:3.500A) Processing helix chain 'e' and resid 522 through 545 Processing helix chain 'e' and resid 552 through 568 removed outlier: 4.521A pdb=" N ASN e 558 " --> pdb=" O GLN e 554 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL e 563 " --> pdb=" O ILE e 559 " (cutoff:3.500A) Processing helix chain 'e' and resid 581 through 589 removed outlier: 3.601A pdb=" N GLN e 586 " --> pdb=" O PRO e 582 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 47 Processing helix chain 'f' and resid 64 through 81 Proline residue: f 74 - end of helix Processing helix chain 'f' and resid 99 through 115 removed outlier: 3.943A pdb=" N MET f 112 " --> pdb=" O ASN f 108 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG f 113 " --> pdb=" O TYR f 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 118 through 130 Processing helix chain 'f' and resid 200 through 204 Processing helix chain 'f' and resid 212 through 216 removed outlier: 3.521A pdb=" N ASP f 215 " --> pdb=" O CYS f 212 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA f 216 " --> pdb=" O ILE f 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 212 through 216' Processing helix chain 'f' and resid 226 through 234 Processing helix chain 'f' and resid 339 through 368 removed outlier: 3.567A pdb=" N LYS f 343 " --> pdb=" O SER f 339 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP f 346 " --> pdb=" O ASP f 342 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE f 347 " --> pdb=" O LYS f 343 " (cutoff:3.500A) Processing helix chain 'f' and resid 379 through 385 Processing helix chain 'f' and resid 409 through 426 removed outlier: 3.557A pdb=" N ARG f 417 " --> pdb=" O GLY f 413 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU f 418 " --> pdb=" O MET f 414 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU f 419 " --> pdb=" O LEU f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 448 through 458 Processing helix chain 'f' and resid 459 through 484 removed outlier: 3.870A pdb=" N LYS f 473 " --> pdb=" O GLU f 469 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG f 474 " --> pdb=" O THR f 470 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU f 479 " --> pdb=" O LEU f 475 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE f 484 " --> pdb=" O HIS f 480 " (cutoff:3.500A) Processing helix chain 'f' and resid 522 through 545 Processing helix chain 'f' and resid 552 through 568 removed outlier: 4.582A pdb=" N ASN f 558 " --> pdb=" O GLN f 554 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL f 563 " --> pdb=" O ILE f 559 " (cutoff:3.500A) Processing helix chain 'f' and resid 581 through 588 removed outlier: 3.524A pdb=" N LEU f 585 " --> pdb=" O SER f 581 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN f 586 " --> pdb=" O PRO f 582 " (cutoff:3.500A) Processing helix chain 'g' and resid 13 through 47 removed outlier: 3.563A pdb=" N ARG g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 64 through 81 removed outlier: 3.530A pdb=" N THR g 68 " --> pdb=" O ASP g 64 " (cutoff:3.500A) Proline residue: g 74 - end of helix Processing helix chain 'g' and resid 99 through 115 removed outlier: 3.925A pdb=" N MET g 112 " --> pdb=" O ASN g 108 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG g 113 " --> pdb=" O TYR g 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN g 115 " --> pdb=" O PHE g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 130 Processing helix chain 'g' and resid 200 through 204 Processing helix chain 'g' and resid 212 through 216 removed outlier: 3.692A pdb=" N ASP g 215 " --> pdb=" O CYS g 212 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA g 216 " --> pdb=" O ILE g 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 212 through 216' Processing helix chain 'g' and resid 226 through 234 Processing helix chain 'g' and resid 340 through 368 removed outlier: 7.018A pdb=" N ASP g 346 " --> pdb=" O ASP g 342 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE g 347 " --> pdb=" O LYS g 343 " (cutoff:3.500A) Processing helix chain 'g' and resid 379 through 385 removed outlier: 3.583A pdb=" N LEU g 383 " --> pdb=" O GLU g 380 " (cutoff:3.500A) Processing helix chain 'g' and resid 408 through 410 No H-bonds generated for 'chain 'g' and resid 408 through 410' Processing helix chain 'g' and resid 411 through 426 removed outlier: 3.639A pdb=" N GLU g 419 " --> pdb=" O LEU g 415 " (cutoff:3.500A) Processing helix chain 'g' and resid 448 through 458 Processing helix chain 'g' and resid 458 through 484 removed outlier: 4.293A pdb=" N LEU g 462 " --> pdb=" O GLN g 458 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS g 473 " --> pdb=" O GLU g 469 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG g 474 " --> pdb=" O THR g 470 " (cutoff:3.500A) Processing helix chain 'g' and resid 522 through 545 Processing helix chain 'g' and resid 552 through 568 removed outlier: 4.429A pdb=" N ASN g 558 " --> pdb=" O GLN g 554 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL g 563 " --> pdb=" O ILE g 559 " (cutoff:3.500A) Processing helix chain 'g' and resid 581 through 589 Processing sheet with id=AA1, first strand: chain 'k' and resid 136 through 142 Processing sheet with id=AA2, first strand: chain 'k' and resid 219 through 223 Processing sheet with id=AA3, first strand: chain 'k' and resid 369 through 371 removed outlier: 4.168A pdb=" N THR k 400 " --> pdb=" O VAL k 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'j' and resid 136 through 142 Processing sheet with id=AA5, first strand: chain 'j' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'j' and resid 369 through 371 removed outlier: 4.061A pdb=" N THR j 400 " --> pdb=" O VAL j 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 136 through 143 removed outlier: 4.075A pdb=" N LYS i 191 " --> pdb=" O VAL i 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'i' and resid 219 through 223 removed outlier: 3.584A pdb=" N LEU i 302 " --> pdb=" O TRP i 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'h' and resid 136 through 142 Processing sheet with id=AB1, first strand: chain 'h' and resid 219 through 223 Processing sheet with id=AB2, first strand: chain 'l' and resid 136 through 142 Processing sheet with id=AB3, first strand: chain 'l' and resid 219 through 223 Processing sheet with id=AB4, first strand: chain 'l' and resid 369 through 371 removed outlier: 3.821A pdb=" N THR l 400 " --> pdb=" O VAL l 371 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 136 through 142 Processing sheet with id=AB6, first strand: chain 'a' and resid 219 through 223 Processing sheet with id=AB7, first strand: chain 'a' and resid 369 through 371 removed outlier: 4.103A pdb=" N THR a 400 " --> pdb=" O VAL a 371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 136 through 142 Processing sheet with id=AB9, first strand: chain 'b' and resid 219 through 223 Processing sheet with id=AC1, first strand: chain 'b' and resid 369 through 371 removed outlier: 4.138A pdb=" N THR b 400 " --> pdb=" O VAL b 371 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 136 through 142 Processing sheet with id=AC3, first strand: chain 'c' and resid 219 through 223 Processing sheet with id=AC4, first strand: chain 'c' and resid 369 through 371 removed outlier: 3.904A pdb=" N THR c 400 " --> pdb=" O VAL c 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 136 through 142 Processing sheet with id=AC6, first strand: chain 'd' and resid 219 through 223 Processing sheet with id=AC7, first strand: chain 'd' and resid 369 through 371 removed outlier: 3.993A pdb=" N THR d 400 " --> pdb=" O VAL d 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 136 through 142 Processing sheet with id=AC9, first strand: chain 'e' and resid 218 through 223 Processing sheet with id=AD1, first strand: chain 'e' and resid 369 through 371 removed outlier: 3.722A pdb=" N THR e 400 " --> pdb=" O VAL e 371 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 136 through 142 Processing sheet with id=AD3, first strand: chain 'f' and resid 218 through 223 removed outlier: 3.612A pdb=" N LEU f 302 " --> pdb=" O TRP f 318 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'f' and resid 369 through 371 removed outlier: 3.884A pdb=" N THR f 400 " --> pdb=" O VAL f 371 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'g' and resid 136 through 142 Processing sheet with id=AD6, first strand: chain 'g' and resid 218 through 223 2255 hydrogen bonds defined for protein. 6462 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: 14.80 Time building geometry restraints manager: 20.30 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: 16325 1.34 - 1.46: 8988 1.46 - 1.58: 23241 1.58 - 1.70: 0 1.70 - 1.82: 510 Bond restraints: 49064 Sorted by residual: bond pdb=" CA GLU h 95 " pdb=" CB GLU h 95 " ideal model delta sigma weight residual 1.526 1.568 -0.042 1.70e-02 3.46e+03 6.01e+00 bond pdb=" C ASN l 503 " pdb=" N PRO l 504 " ideal model delta sigma weight residual 1.328 1.358 -0.030 1.25e-02 6.40e+03 5.77e+00 bond pdb=" C ASN k 503 " pdb=" N PRO k 504 " ideal model delta sigma weight residual 1.328 1.356 -0.028 1.26e-02 6.30e+03 4.99e+00 bond pdb=" C ASN j 503 " pdb=" N PRO j 504 " ideal model delta sigma weight residual 1.328 1.355 -0.027 1.25e-02 6.40e+03 4.67e+00 bond pdb=" CA MET d 131 " pdb=" C MET d 131 " ideal model delta sigma weight residual 1.524 1.560 -0.035 1.66e-02 3.63e+03 4.52e+00 ... (remaining 49059 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.56: 827 105.56 - 112.71: 25056 112.71 - 119.86: 17702 119.86 - 127.01: 22098 127.01 - 134.15: 490 Bond angle restraints: 66173 Sorted by residual: angle pdb=" N VAL f 492 " pdb=" CA VAL f 492 " pdb=" C VAL f 492 " ideal model delta sigma weight residual 112.83 104.65 8.18 9.90e-01 1.02e+00 6.82e+01 angle pdb=" CA MET d 131 " pdb=" C MET d 131 " pdb=" N LYS d 132 " ideal model delta sigma weight residual 117.96 112.46 5.50 1.23e+00 6.61e-01 2.00e+01 angle pdb=" CA MET j 532 " pdb=" CB MET j 532 " pdb=" CG MET j 532 " ideal model delta sigma weight residual 114.10 122.76 -8.66 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CB MET k 537 " pdb=" CG MET k 537 " pdb=" SD MET k 537 " ideal model delta sigma weight residual 112.70 125.12 -12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB MET j 532 " pdb=" CG MET j 532 " pdb=" SD MET j 532 " ideal model delta sigma weight residual 112.70 125.11 -12.41 3.00e+00 1.11e-01 1.71e+01 ... (remaining 66168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 26134 17.03 - 34.05: 3197 34.05 - 51.08: 476 51.08 - 68.11: 66 68.11 - 85.13: 40 Dihedral angle restraints: 29913 sinusoidal: 12574 harmonic: 17339 Sorted by residual: dihedral pdb=" CA ILE g 519 " pdb=" C ILE g 519 " pdb=" N GLY g 520 " pdb=" CA GLY g 520 " ideal model delta harmonic sigma weight residual 180.00 147.75 32.25 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA ILE l 519 " pdb=" C ILE l 519 " pdb=" N GLY l 520 " pdb=" CA GLY l 520 " ideal model delta harmonic sigma weight residual 180.00 149.34 30.66 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA VAL k 515 " pdb=" C VAL k 515 " pdb=" N THR k 516 " pdb=" CA THR k 516 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 29910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6257 0.067 - 0.135: 909 0.135 - 0.202: 62 0.202 - 0.269: 8 0.269 - 0.337: 3 Chirality restraints: 7239 Sorted by residual: chirality pdb=" CG LEU l 529 " pdb=" CB LEU l 529 " pdb=" CD1 LEU l 529 " pdb=" CD2 LEU l 529 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB ILE i 484 " pdb=" CA ILE i 484 " pdb=" CG1 ILE i 484 " pdb=" CG2 ILE i 484 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE l 484 " pdb=" CA ILE l 484 " pdb=" CG1 ILE l 484 " pdb=" CG2 ILE l 484 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 7236 not shown) Planarity restraints: 8652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP i 71 " -0.026 2.00e-02 2.50e+03 2.62e-02 1.72e+01 pdb=" CG TRP i 71 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP i 71 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP i 71 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP i 71 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP i 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP i 71 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 71 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 71 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP i 71 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG a 54 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO a 55 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO a 55 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO a 55 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN g 503 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO g 504 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO g 504 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO g 504 " 0.038 5.00e-02 4.00e+02 ... (remaining 8649 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1247 2.66 - 3.22: 51656 3.22 - 3.78: 80853 3.78 - 4.34: 106099 4.34 - 4.90: 164447 Nonbonded interactions: 404302 Sorted by model distance: nonbonded pdb=" O LEU f 129 " pdb=" OG SER f 339 " model vdw 2.097 2.440 nonbonded pdb=" O LYS h 561 " pdb=" OG1 THR h 564 " model vdw 2.136 2.440 nonbonded pdb=" O SER h 31 " pdb=" OG SER h 35 " model vdw 2.151 2.440 nonbonded pdb=" ND2 ASN k 578 " pdb=" O VAL l 549 " model vdw 2.173 2.520 nonbonded pdb=" NH1 ARG a 533 " pdb=" OE2 GLU a 536 " model vdw 2.176 2.520 ... (remaining 404297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and (resid 9 through 366 or resid 405 through 595)) selection = (chain 'b' and (resid 9 through 366 or resid 405 through 595)) selection = (chain 'c' and (resid 9 through 366 or resid 405 through 595)) selection = (chain 'd' and (resid 9 through 366 or resid 405 through 595)) selection = (chain 'e' and (resid 9 through 366 or resid 405 through 595)) selection = (chain 'f' and (resid 9 through 366 or resid 405 through 595)) selection = (chain 'g' and (resid 9 through 366 or resid 405 through 595)) selection = chain 'h' selection = (chain 'i' and (resid 9 through 366 or resid 405 through 595)) selection = (chain 'j' and (resid 9 through 366 or resid 405 through 595)) selection = (chain 'k' and (resid 9 through 366 or resid 405 through 595)) selection = (chain 'l' and (resid 9 through 366 or resid 405 through 595)) } 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 3.610 Check model and map are aligned: 0.750 Set scattering table: 0.460 Process input model: 110.960 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.003 0.047 49064 Z= 0.196 Angle : 0.792 12.419 66173 Z= 0.426 Chirality : 0.046 0.337 7239 Planarity : 0.005 0.097 8652 Dihedral : 14.411 85.132 18699 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 25.58 Ramachandran Plot: Outliers : 0.72 % Allowed : 18.81 % Favored : 80.47 % Rotamer: Outliers : 0.02 % Allowed : 0.32 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.11), residues: 5869 helix: -0.77 (0.10), residues: 2500 sheet: -0.43 (0.27), residues: 496 loop : -3.87 (0.11), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP i 71 HIS 0.012 0.001 HIS k 482 PHE 0.033 0.001 PHE d 476 TYR 0.022 0.001 TYR g 569 ARG 0.010 0.000 ARG l 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 5.517 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: k 73 MET cc_start: 0.9667 (tpt) cc_final: 0.8930 (tpp) REVERT: k 338 MET cc_start: 0.8000 (ppp) cc_final: 0.7380 (ppp) REVERT: k 467 PHE cc_start: 0.8995 (m-80) cc_final: 0.8763 (m-80) REVERT: k 530 HIS cc_start: 0.9285 (m90) cc_final: 0.8671 (m-70) REVERT: j 76 LEU cc_start: 0.9896 (mt) cc_final: 0.9666 (mt) REVERT: j 77 MET cc_start: 0.9848 (mmp) cc_final: 0.9495 (mmp) REVERT: j 79 VAL cc_start: 0.9460 (m) cc_final: 0.9197 (m) REVERT: j 338 MET cc_start: 0.7988 (ppp) cc_final: 0.7726 (ppp) REVERT: j 486 TYR cc_start: 0.7819 (t80) cc_final: 0.6760 (t80) REVERT: j 534 ILE cc_start: 0.8245 (pt) cc_final: 0.7660 (pt) REVERT: j 537 MET cc_start: 0.9179 (mpp) cc_final: 0.8898 (mpp) REVERT: i 73 MET cc_start: 0.9710 (mmp) cc_final: 0.9473 (mmm) REVERT: i 112 MET cc_start: 0.9780 (mmt) cc_final: 0.9545 (mmm) REVERT: h 355 MET cc_start: 0.5763 (mmp) cc_final: 0.5402 (mmm) REVERT: h 359 MET cc_start: 0.8702 (mpp) cc_final: 0.8348 (ptp) REVERT: h 522 MET cc_start: 0.6773 (ppp) cc_final: 0.6419 (ppp) REVERT: l 73 MET cc_start: 0.9398 (tpp) cc_final: 0.8788 (tpp) REVERT: l 80 PHE cc_start: 0.9251 (m-80) cc_final: 0.8810 (m-80) REVERT: l 112 MET cc_start: 0.9699 (mmp) cc_final: 0.9408 (mmp) REVERT: l 447 MET cc_start: 0.8434 (mmp) cc_final: 0.8218 (mmp) REVERT: l 466 MET cc_start: 0.9322 (ptt) cc_final: 0.9052 (ppp) REVERT: l 480 HIS cc_start: 0.9258 (m-70) cc_final: 0.8912 (m-70) REVERT: a 77 MET cc_start: 0.9580 (mmp) cc_final: 0.9325 (mmm) REVERT: a 80 PHE cc_start: 0.8984 (m-80) cc_final: 0.8226 (m-80) REVERT: a 112 MET cc_start: 0.9806 (mmm) cc_final: 0.9329 (tpp) REVERT: a 127 ASP cc_start: 0.9554 (m-30) cc_final: 0.9335 (m-30) REVERT: a 338 MET cc_start: 0.9216 (ppp) cc_final: 0.8807 (ppp) REVERT: a 467 PHE cc_start: 0.9277 (m-80) cc_final: 0.8813 (m-80) REVERT: a 476 PHE cc_start: 0.9593 (t80) cc_final: 0.9128 (t80) REVERT: a 530 HIS cc_start: 0.9453 (m90) cc_final: 0.9189 (m-70) REVERT: b 73 MET cc_start: 0.9464 (tpt) cc_final: 0.8628 (tpp) REVERT: b 127 ASP cc_start: 0.9026 (m-30) cc_final: 0.8635 (m-30) REVERT: b 131 MET cc_start: 0.7539 (ttt) cc_final: 0.6708 (ppp) REVERT: b 338 MET cc_start: 0.9028 (ppp) cc_final: 0.8769 (ppp) REVERT: b 480 HIS cc_start: 0.9352 (t-90) cc_final: 0.9146 (t70) REVERT: b 534 ILE cc_start: 0.9510 (pt) cc_final: 0.9226 (pt) REVERT: c 77 MET cc_start: 0.9561 (mmp) cc_final: 0.9260 (mmp) REVERT: c 130 MET cc_start: 0.9164 (tpt) cc_final: 0.8397 (tpt) REVERT: c 338 MET cc_start: 0.9437 (ppp) cc_final: 0.8938 (ppp) REVERT: c 466 MET cc_start: 0.8442 (ppp) cc_final: 0.8234 (ppp) REVERT: d 121 MET cc_start: 0.9708 (ppp) cc_final: 0.9455 (ppp) REVERT: d 131 MET cc_start: 0.7249 (ttt) cc_final: 0.7007 (ttt) REVERT: d 338 MET cc_start: 0.8627 (ppp) cc_final: 0.7750 (ppp) REVERT: d 396 MET cc_start: 0.3586 (ttt) cc_final: 0.3352 (ttt) REVERT: d 467 PHE cc_start: 0.9446 (m-80) cc_final: 0.8925 (m-80) REVERT: e 77 MET cc_start: 0.9292 (mmp) cc_final: 0.8981 (mmm) REVERT: e 338 MET cc_start: 0.7201 (ppp) cc_final: 0.6433 (ppp) REVERT: f 112 MET cc_start: 0.5624 (tmm) cc_final: 0.5347 (tmm) REVERT: g 76 LEU cc_start: 0.5120 (mt) cc_final: 0.4855 (mt) REVERT: g 77 MET cc_start: 0.7570 (tmm) cc_final: 0.6935 (ptt) outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.5728 time to fit residues: 437.2183 Evaluate side-chains 368 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 5.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 499 optimal weight: 30.0000 chunk 448 optimal weight: 40.0000 chunk 248 optimal weight: 6.9990 chunk 153 optimal weight: 30.0000 chunk 302 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 464 optimal weight: 0.1980 chunk 179 optimal weight: 8.9990 chunk 282 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 537 optimal weight: 30.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 554 GLN ** j 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 530 HIS ** j 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 554 GLN ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 480 HIS a 506 ASN a 558 ASN ** b 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 527 GLN ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 49064 Z= 0.194 Angle : 0.691 8.766 66173 Z= 0.367 Chirality : 0.044 0.201 7239 Planarity : 0.005 0.068 8652 Dihedral : 5.351 31.341 6541 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 24.90 Ramachandran Plot: Outliers : 0.70 % Allowed : 18.90 % Favored : 80.41 % Rotamer: Outliers : 0.15 % Allowed : 7.70 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.11), residues: 5869 helix: -0.53 (0.10), residues: 2547 sheet: -0.10 (0.28), residues: 453 loop : -3.86 (0.11), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP h 124 HIS 0.010 0.001 HIS k 482 PHE 0.025 0.001 PHE a 476 TYR 0.018 0.001 TYR f 106 ARG 0.006 0.000 ARG g 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 446 time to evaluate : 5.559 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: symmetry clash revert: symmetry clash REVERT: k 73 MET cc_start: 0.9642 (tpt) cc_final: 0.9020 (tpp) REVERT: k 77 MET cc_start: 0.9628 (mmp) cc_final: 0.9299 (mmp) REVERT: k 467 PHE cc_start: 0.9112 (m-80) cc_final: 0.8575 (m-80) REVERT: k 480 HIS cc_start: 0.9506 (t70) cc_final: 0.9261 (t70) REVERT: k 530 HIS cc_start: 0.9289 (m90) cc_final: 0.8773 (m-70) REVERT: k 537 MET cc_start: 0.9720 (ttp) cc_final: 0.9381 (mtp) REVERT: j 77 MET cc_start: 0.9849 (mmp) cc_final: 0.9640 (mmp) REVERT: j 79 VAL cc_start: 0.9466 (m) cc_final: 0.9172 (m) REVERT: j 338 MET cc_start: 0.7895 (ppp) cc_final: 0.7416 (ppp) REVERT: j 467 PHE cc_start: 0.9435 (m-80) cc_final: 0.8689 (m-80) REVERT: i 71 TRP cc_start: 0.8470 (m-90) cc_final: 0.8195 (m-10) REVERT: i 73 MET cc_start: 0.9720 (mmp) cc_final: 0.9468 (mmm) REVERT: i 112 MET cc_start: 0.9719 (mmt) cc_final: 0.9442 (mmm) REVERT: h 95 GLU cc_start: 0.9619 (tp30) cc_final: 0.9386 (tp30) REVERT: h 355 MET cc_start: 0.5933 (mmp) cc_final: 0.5594 (mmm) REVERT: h 359 MET cc_start: 0.8349 (mpp) cc_final: 0.7948 (ptp) REVERT: l 73 MET cc_start: 0.9435 (tpp) cc_final: 0.8775 (tpp) REVERT: l 77 MET cc_start: 0.9797 (mmp) cc_final: 0.9586 (mmp) REVERT: l 80 PHE cc_start: 0.9217 (m-80) cc_final: 0.8796 (m-80) REVERT: l 127 ASP cc_start: 0.8987 (m-30) cc_final: 0.8770 (m-30) REVERT: l 130 MET cc_start: 0.9216 (mpp) cc_final: 0.8986 (tpt) REVERT: l 338 MET cc_start: 0.8530 (ppp) cc_final: 0.8308 (ppp) REVERT: l 447 MET cc_start: 0.8455 (mmp) cc_final: 0.8239 (mmp) REVERT: l 466 MET cc_start: 0.9541 (ptt) cc_final: 0.9104 (ppp) REVERT: l 480 HIS cc_start: 0.9178 (m-70) cc_final: 0.8816 (m-70) REVERT: l 530 HIS cc_start: 0.9316 (m90) cc_final: 0.9078 (m-70) REVERT: a 73 MET cc_start: 0.9383 (tpp) cc_final: 0.8374 (tpp) REVERT: a 77 MET cc_start: 0.9680 (mmp) cc_final: 0.9148 (mmp) REVERT: a 79 VAL cc_start: 0.9678 (p) cc_final: 0.9425 (p) REVERT: a 80 PHE cc_start: 0.9195 (m-80) cc_final: 0.8494 (m-80) REVERT: a 112 MET cc_start: 0.9800 (mmm) cc_final: 0.9547 (tpt) REVERT: a 338 MET cc_start: 0.9219 (ppp) cc_final: 0.8819 (ppp) REVERT: a 363 TYR cc_start: 0.9418 (m-80) cc_final: 0.9169 (m-10) REVERT: a 467 PHE cc_start: 0.9024 (m-80) cc_final: 0.8609 (m-80) REVERT: a 476 PHE cc_start: 0.9531 (t80) cc_final: 0.9004 (t80) REVERT: b 73 MET cc_start: 0.9483 (tpt) cc_final: 0.8619 (tpp) REVERT: b 480 HIS cc_start: 0.9369 (t-90) cc_final: 0.9156 (t70) REVERT: b 534 ILE cc_start: 0.9519 (pt) cc_final: 0.9227 (pt) REVERT: c 77 MET cc_start: 0.9616 (mmp) cc_final: 0.9154 (mmp) REVERT: c 130 MET cc_start: 0.9357 (tpt) cc_final: 0.8639 (tpt) REVERT: c 338 MET cc_start: 0.9413 (ppp) cc_final: 0.8927 (ppp) REVERT: c 476 PHE cc_start: 0.9201 (t80) cc_final: 0.8792 (t80) REVERT: c 524 LYS cc_start: 0.9466 (tppt) cc_final: 0.9095 (tppt) REVERT: d 72 ILE cc_start: 0.9751 (pt) cc_final: 0.9550 (pt) REVERT: d 73 MET cc_start: 0.9257 (tpp) cc_final: 0.8641 (tpp) REVERT: d 77 MET cc_start: 0.9547 (mmp) cc_final: 0.9311 (mmm) REVERT: d 121 MET cc_start: 0.9735 (ppp) cc_final: 0.9531 (ppp) REVERT: d 338 MET cc_start: 0.9049 (ppp) cc_final: 0.8638 (ppp) REVERT: d 396 MET cc_start: 0.3632 (ttt) cc_final: 0.3402 (ttt) REVERT: d 476 PHE cc_start: 0.9432 (t80) cc_final: 0.9147 (t80) REVERT: d 480 HIS cc_start: 0.9486 (t70) cc_final: 0.9215 (t70) REVERT: e 77 MET cc_start: 0.9329 (mmp) cc_final: 0.9002 (mmm) REVERT: e 121 MET cc_start: 0.8858 (ppp) cc_final: 0.8655 (ppp) REVERT: e 338 MET cc_start: 0.7680 (ppp) cc_final: 0.7042 (ppp) REVERT: f 462 LEU cc_start: 0.9193 (mp) cc_final: 0.8982 (mp) REVERT: g 77 MET cc_start: 0.7342 (tmm) cc_final: 0.6903 (ptt) outliers start: 8 outliers final: 1 residues processed: 454 average time/residue: 0.5899 time to fit residues: 454.0367 Evaluate side-chains 370 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 369 time to evaluate : 5.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 298 optimal weight: 30.0000 chunk 166 optimal weight: 30.0000 chunk 447 optimal weight: 9.9990 chunk 366 optimal weight: 0.1980 chunk 148 optimal weight: 20.0000 chunk 538 optimal weight: 5.9990 chunk 581 optimal weight: 50.0000 chunk 479 optimal weight: 30.0000 chunk 534 optimal weight: 0.1980 chunk 183 optimal weight: 8.9990 chunk 432 optimal weight: 30.0000 overall best weight: 5.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 530 HIS ** j 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 480 HIS ** h 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 558 ASN ** b 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 14 GLN ** c 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 49064 Z= 0.199 Angle : 0.695 9.992 66173 Z= 0.368 Chirality : 0.044 0.211 7239 Planarity : 0.005 0.070 8652 Dihedral : 5.355 31.302 6541 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.72 % Allowed : 18.98 % Favored : 80.30 % Rotamer: Outliers : 0.04 % Allowed : 5.95 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.11), residues: 5869 helix: -0.47 (0.10), residues: 2544 sheet: -0.12 (0.28), residues: 448 loop : -3.89 (0.11), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP h 124 HIS 0.011 0.001 HIS a 530 PHE 0.025 0.001 PHE c 476 TYR 0.024 0.001 TYR c 363 ARG 0.007 0.000 ARG g 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 434 time to evaluate : 5.439 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 73 MET cc_start: 0.9664 (tpt) cc_final: 0.9115 (tpp) REVERT: k 77 MET cc_start: 0.9649 (mmp) cc_final: 0.9330 (mmp) REVERT: k 80 PHE cc_start: 0.9132 (m-80) cc_final: 0.8812 (m-80) REVERT: k 127 ASP cc_start: 0.9451 (m-30) cc_final: 0.9240 (m-30) REVERT: k 466 MET cc_start: 0.9479 (ppp) cc_final: 0.9246 (ppp) REVERT: k 467 PHE cc_start: 0.9167 (m-80) cc_final: 0.8707 (m-80) REVERT: k 480 HIS cc_start: 0.9518 (t70) cc_final: 0.9277 (t70) REVERT: k 530 HIS cc_start: 0.9309 (m90) cc_final: 0.8812 (m-70) REVERT: k 537 MET cc_start: 0.9690 (ttp) cc_final: 0.9341 (mtp) REVERT: j 70 ASP cc_start: 0.9214 (m-30) cc_final: 0.9007 (m-30) REVERT: j 73 MET cc_start: 0.9574 (mmp) cc_final: 0.9323 (tpp) REVERT: j 77 MET cc_start: 0.9686 (mmp) cc_final: 0.9211 (mmp) REVERT: j 338 MET cc_start: 0.7939 (ppp) cc_final: 0.7517 (ppp) REVERT: j 467 PHE cc_start: 0.9453 (m-80) cc_final: 0.8787 (m-80) REVERT: j 480 HIS cc_start: 0.9509 (t70) cc_final: 0.9200 (t70) REVERT: i 73 MET cc_start: 0.9697 (mmp) cc_final: 0.9434 (mmm) REVERT: i 112 MET cc_start: 0.9739 (mmt) cc_final: 0.9492 (mmm) REVERT: h 95 GLU cc_start: 0.9602 (tp30) cc_final: 0.9353 (tp30) REVERT: h 359 MET cc_start: 0.8351 (mpp) cc_final: 0.8026 (ptp) REVERT: h 522 MET cc_start: 0.7229 (ppp) cc_final: 0.7001 (ppp) REVERT: l 10 MET cc_start: 0.8690 (mpp) cc_final: 0.8439 (mpp) REVERT: l 73 MET cc_start: 0.9373 (tpp) cc_final: 0.8523 (tpp) REVERT: l 77 MET cc_start: 0.9805 (mmp) cc_final: 0.9523 (mmp) REVERT: l 80 PHE cc_start: 0.9275 (m-80) cc_final: 0.9075 (m-80) REVERT: l 130 MET cc_start: 0.9360 (mpp) cc_final: 0.9084 (tpt) REVERT: l 338 MET cc_start: 0.8749 (ppp) cc_final: 0.8427 (ppp) REVERT: l 447 MET cc_start: 0.8470 (mmp) cc_final: 0.8259 (mmp) REVERT: l 466 MET cc_start: 0.9543 (ptt) cc_final: 0.8731 (ppp) REVERT: l 467 PHE cc_start: 0.9632 (m-80) cc_final: 0.9025 (m-80) REVERT: l 480 HIS cc_start: 0.9232 (m-70) cc_final: 0.8909 (m-70) REVERT: l 482 HIS cc_start: 0.9142 (p-80) cc_final: 0.8842 (p90) REVERT: l 530 HIS cc_start: 0.9397 (m90) cc_final: 0.8958 (m90) REVERT: l 562 GLU cc_start: 0.9755 (OUTLIER) cc_final: 0.9484 (mp0) REVERT: a 73 MET cc_start: 0.9383 (tpp) cc_final: 0.8234 (tpp) REVERT: a 77 MET cc_start: 0.9758 (mmp) cc_final: 0.9082 (mmp) REVERT: a 79 VAL cc_start: 0.9728 (p) cc_final: 0.9461 (p) REVERT: a 80 PHE cc_start: 0.9262 (m-80) cc_final: 0.8735 (m-80) REVERT: a 112 MET cc_start: 0.9811 (mmm) cc_final: 0.9520 (tpt) REVERT: a 338 MET cc_start: 0.9419 (ppp) cc_final: 0.9039 (ppp) REVERT: a 363 TYR cc_start: 0.9481 (m-80) cc_final: 0.9199 (m-10) REVERT: a 466 MET cc_start: 0.9268 (ppp) cc_final: 0.8997 (ppp) REVERT: a 467 PHE cc_start: 0.8944 (m-80) cc_final: 0.8605 (m-80) REVERT: a 476 PHE cc_start: 0.9429 (t80) cc_final: 0.8906 (t80) REVERT: b 73 MET cc_start: 0.9484 (tpt) cc_final: 0.8613 (tpp) REVERT: b 112 MET cc_start: 0.9725 (mmm) cc_final: 0.9491 (mmm) REVERT: b 467 PHE cc_start: 0.9237 (m-10) cc_final: 0.8806 (m-80) REVERT: b 534 ILE cc_start: 0.9534 (pt) cc_final: 0.9242 (pt) REVERT: c 77 MET cc_start: 0.9684 (mmp) cc_final: 0.9214 (mmp) REVERT: c 130 MET cc_start: 0.9422 (tpt) cc_final: 0.8744 (tpt) REVERT: c 338 MET cc_start: 0.9423 (ppp) cc_final: 0.9071 (ppp) REVERT: c 466 MET cc_start: 0.8511 (ppp) cc_final: 0.8086 (ppp) REVERT: c 467 PHE cc_start: 0.8660 (m-10) cc_final: 0.7973 (m-80) REVERT: c 524 LYS cc_start: 0.9396 (tppt) cc_final: 0.9075 (tppt) REVERT: d 121 MET cc_start: 0.9729 (ppp) cc_final: 0.9528 (ppp) REVERT: d 131 MET cc_start: 0.7255 (ttt) cc_final: 0.7011 (ttt) REVERT: d 338 MET cc_start: 0.9080 (ppp) cc_final: 0.8702 (ppp) REVERT: d 466 MET cc_start: 0.9262 (ppp) cc_final: 0.8738 (ppp) REVERT: d 467 PHE cc_start: 0.9487 (m-10) cc_final: 0.9066 (m-80) REVERT: d 476 PHE cc_start: 0.9459 (t80) cc_final: 0.9181 (t80) REVERT: d 482 HIS cc_start: 0.8581 (m-70) cc_final: 0.8176 (p90) REVERT: e 77 MET cc_start: 0.9350 (mmp) cc_final: 0.8990 (mmm) REVERT: e 121 MET cc_start: 0.8947 (ppp) cc_final: 0.8745 (ppp) REVERT: e 338 MET cc_start: 0.7789 (ppp) cc_final: 0.7218 (ppp) outliers start: 2 outliers final: 0 residues processed: 436 average time/residue: 0.5615 time to fit residues: 414.0573 Evaluate side-chains 367 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 366 time to evaluate : 5.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 532 optimal weight: 50.0000 chunk 404 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 361 optimal weight: 4.9990 chunk 540 optimal weight: 20.0000 chunk 572 optimal weight: 9.9990 chunk 282 optimal weight: 0.9980 chunk 512 optimal weight: 7.9990 chunk 154 optimal weight: 40.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 24 ASN ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 52 ASN ** j 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 530 HIS j 566 ASN ** j 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 480 HIS ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 506 ASN ** l 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 558 ASN ** a 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 49064 Z= 0.215 Angle : 0.702 10.412 66173 Z= 0.371 Chirality : 0.044 0.222 7239 Planarity : 0.005 0.074 8652 Dihedral : 5.384 30.755 6541 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 28.21 Ramachandran Plot: Outliers : 0.68 % Allowed : 19.22 % Favored : 80.10 % Rotamer: Outliers : 0.11 % Allowed : 5.53 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.11), residues: 5869 helix: -0.45 (0.10), residues: 2550 sheet: -0.10 (0.28), residues: 442 loop : -3.91 (0.10), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP i 71 HIS 0.009 0.001 HIS a 530 PHE 0.025 0.001 PHE a 476 TYR 0.019 0.001 TYR c 363 ARG 0.008 0.000 ARG l 422 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 433 time to evaluate : 5.528 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 73 MET cc_start: 0.9671 (tpt) cc_final: 0.8955 (tpp) REVERT: k 77 MET cc_start: 0.9702 (mmp) cc_final: 0.9213 (mmt) REVERT: k 80 PHE cc_start: 0.9290 (m-80) cc_final: 0.9024 (m-80) REVERT: k 466 MET cc_start: 0.9506 (ppp) cc_final: 0.9241 (ppp) REVERT: k 467 PHE cc_start: 0.9208 (m-80) cc_final: 0.8757 (m-80) REVERT: k 480 HIS cc_start: 0.9539 (t70) cc_final: 0.9312 (t70) REVERT: k 530 HIS cc_start: 0.9300 (m90) cc_final: 0.8797 (m-70) REVERT: k 534 ILE cc_start: 0.9197 (pt) cc_final: 0.8764 (pt) REVERT: k 537 MET cc_start: 0.9739 (ttp) cc_final: 0.9397 (mtp) REVERT: j 70 ASP cc_start: 0.9186 (m-30) cc_final: 0.8927 (m-30) REVERT: j 73 MET cc_start: 0.9566 (mmp) cc_final: 0.9132 (tpp) REVERT: j 77 MET cc_start: 0.9729 (mmp) cc_final: 0.9405 (mmm) REVERT: j 338 MET cc_start: 0.8003 (ppp) cc_final: 0.7587 (ppp) REVERT: j 467 PHE cc_start: 0.9491 (m-80) cc_final: 0.8839 (m-80) REVERT: j 480 HIS cc_start: 0.9436 (t70) cc_final: 0.9192 (t70) REVERT: j 580 ASN cc_start: 0.9134 (m110) cc_final: 0.8906 (m-40) REVERT: i 71 TRP cc_start: 0.8554 (m-90) cc_final: 0.8325 (m-90) REVERT: i 73 MET cc_start: 0.9695 (mmp) cc_final: 0.9438 (mmm) REVERT: i 112 MET cc_start: 0.9722 (mmt) cc_final: 0.9464 (mmm) REVERT: h 95 GLU cc_start: 0.9597 (tp30) cc_final: 0.9348 (tp30) REVERT: h 355 MET cc_start: 0.6180 (mmp) cc_final: 0.5931 (mmm) REVERT: h 359 MET cc_start: 0.8319 (mpp) cc_final: 0.7949 (ptp) REVERT: l 10 MET cc_start: 0.8745 (mpp) cc_final: 0.8497 (mpp) REVERT: l 73 MET cc_start: 0.9367 (tpp) cc_final: 0.8487 (tpp) REVERT: l 77 MET cc_start: 0.9804 (mmp) cc_final: 0.9488 (mmp) REVERT: l 78 LYS cc_start: 0.9420 (mmpt) cc_final: 0.9220 (mmmt) REVERT: l 80 PHE cc_start: 0.9288 (m-80) cc_final: 0.9077 (m-80) REVERT: l 130 MET cc_start: 0.9406 (mpp) cc_final: 0.9118 (tpt) REVERT: l 338 MET cc_start: 0.8851 (ppp) cc_final: 0.8545 (ppp) REVERT: l 466 MET cc_start: 0.9541 (ptt) cc_final: 0.8781 (ppp) REVERT: l 467 PHE cc_start: 0.9640 (m-80) cc_final: 0.9217 (m-80) REVERT: l 480 HIS cc_start: 0.9166 (m-70) cc_final: 0.8874 (m-70) REVERT: l 482 HIS cc_start: 0.9155 (p-80) cc_final: 0.8951 (p90) REVERT: l 530 HIS cc_start: 0.9190 (m90) cc_final: 0.8874 (m-70) REVERT: a 73 MET cc_start: 0.9355 (tpp) cc_final: 0.8204 (tpp) REVERT: a 77 MET cc_start: 0.9794 (mmp) cc_final: 0.9101 (mmp) REVERT: a 79 VAL cc_start: 0.9740 (p) cc_final: 0.9500 (m) REVERT: a 112 MET cc_start: 0.9793 (mmm) cc_final: 0.9291 (mmm) REVERT: a 338 MET cc_start: 0.9424 (ppp) cc_final: 0.9081 (ppp) REVERT: a 363 TYR cc_start: 0.9503 (m-80) cc_final: 0.9300 (m-80) REVERT: a 466 MET cc_start: 0.9226 (ppp) cc_final: 0.9003 (ppp) REVERT: a 467 PHE cc_start: 0.9109 (m-80) cc_final: 0.8727 (m-80) REVERT: a 476 PHE cc_start: 0.9431 (t80) cc_final: 0.8878 (t80) REVERT: a 480 HIS cc_start: 0.8807 (m-70) cc_final: 0.8524 (m-70) REVERT: b 73 MET cc_start: 0.9521 (tpt) cc_final: 0.8457 (tpp) REVERT: b 466 MET cc_start: 0.9331 (ppp) cc_final: 0.9116 (ppp) REVERT: b 467 PHE cc_start: 0.9319 (m-10) cc_final: 0.8765 (m-80) REVERT: b 480 HIS cc_start: 0.9479 (t70) cc_final: 0.9277 (t70) REVERT: b 534 ILE cc_start: 0.9533 (pt) cc_final: 0.9265 (pt) REVERT: b 537 MET cc_start: 0.9223 (ppp) cc_final: 0.9007 (ppp) REVERT: c 77 MET cc_start: 0.9767 (mmp) cc_final: 0.9314 (mmp) REVERT: c 130 MET cc_start: 0.9433 (tpt) cc_final: 0.8773 (tpt) REVERT: c 338 MET cc_start: 0.9422 (ppp) cc_final: 0.9149 (ppp) REVERT: c 476 PHE cc_start: 0.9273 (t80) cc_final: 0.8739 (t80) REVERT: c 524 LYS cc_start: 0.9433 (tppt) cc_final: 0.9100 (tppt) REVERT: d 73 MET cc_start: 0.9255 (tpp) cc_final: 0.8063 (tpp) REVERT: d 77 MET cc_start: 0.9662 (mmp) cc_final: 0.9227 (mmp) REVERT: d 338 MET cc_start: 0.8975 (ppp) cc_final: 0.8443 (ppp) REVERT: d 466 MET cc_start: 0.9300 (ppp) cc_final: 0.8757 (ppp) REVERT: d 467 PHE cc_start: 0.9454 (m-10) cc_final: 0.9049 (m-80) REVERT: d 476 PHE cc_start: 0.9480 (t80) cc_final: 0.9188 (t80) REVERT: d 482 HIS cc_start: 0.8713 (m-70) cc_final: 0.8254 (p90) REVERT: e 121 MET cc_start: 0.9029 (ppp) cc_final: 0.8823 (ppp) REVERT: e 338 MET cc_start: 0.7799 (ppp) cc_final: 0.7228 (ppp) REVERT: e 447 MET cc_start: 0.6926 (pmm) cc_final: 0.6603 (ttt) REVERT: e 463 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8572 (mm) REVERT: f 462 LEU cc_start: 0.9110 (mp) cc_final: 0.8899 (mp) outliers start: 6 outliers final: 1 residues processed: 438 average time/residue: 0.5559 time to fit residues: 410.5627 Evaluate side-chains 370 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 368 time to evaluate : 5.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 476 optimal weight: 8.9990 chunk 324 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 426 optimal weight: 0.8980 chunk 236 optimal weight: 7.9990 chunk 488 optimal weight: 5.9990 chunk 395 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 292 optimal weight: 0.9990 chunk 513 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 530 HIS i 480 HIS ** i 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 333 HIS ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 558 ASN ** b 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 52 ASN ** c 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 49064 Z= 0.202 Angle : 0.709 10.460 66173 Z= 0.372 Chirality : 0.044 0.220 7239 Planarity : 0.005 0.062 8652 Dihedral : 5.392 30.945 6541 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.68 % Allowed : 19.37 % Favored : 79.95 % Rotamer: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.11), residues: 5869 helix: -0.50 (0.10), residues: 2592 sheet: -0.12 (0.28), residues: 442 loop : -3.89 (0.11), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP i 71 HIS 0.009 0.001 HIS c 480 PHE 0.045 0.001 PHE c 476 TYR 0.022 0.001 TYR k 363 ARG 0.009 0.000 ARG l 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 436 time to evaluate : 4.807 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: 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: k 73 MET cc_start: 0.9701 (tpt) cc_final: 0.8959 (tpp) REVERT: k 77 MET cc_start: 0.9700 (mmp) cc_final: 0.9129 (mmt) REVERT: k 80 PHE cc_start: 0.9304 (m-80) cc_final: 0.9013 (m-80) REVERT: k 127 ASP cc_start: 0.9532 (m-30) cc_final: 0.9297 (m-30) REVERT: k 130 MET cc_start: 0.9374 (ttt) cc_final: 0.8902 (tpt) REVERT: k 466 MET cc_start: 0.9514 (ppp) cc_final: 0.9252 (ppp) REVERT: k 467 PHE cc_start: 0.9263 (m-80) cc_final: 0.8806 (m-80) REVERT: k 480 HIS cc_start: 0.9514 (t70) cc_final: 0.9210 (t70) REVERT: k 522 MET cc_start: 0.9305 (ppp) cc_final: 0.9087 (ppp) REVERT: k 530 HIS cc_start: 0.9311 (m90) cc_final: 0.8794 (m-70) REVERT: k 537 MET cc_start: 0.9739 (ttp) cc_final: 0.9409 (mtp) REVERT: j 70 ASP cc_start: 0.9166 (m-30) cc_final: 0.8918 (m-30) REVERT: j 73 MET cc_start: 0.9595 (mmp) cc_final: 0.9145 (tpp) REVERT: j 77 MET cc_start: 0.9721 (mmp) cc_final: 0.9386 (mmm) REVERT: j 338 MET cc_start: 0.7979 (ppp) cc_final: 0.7597 (ppp) REVERT: j 467 PHE cc_start: 0.9493 (m-80) cc_final: 0.8827 (m-80) REVERT: i 73 MET cc_start: 0.9665 (mmp) cc_final: 0.9451 (mmm) REVERT: i 112 MET cc_start: 0.9720 (mmt) cc_final: 0.9454 (mmm) REVERT: h 355 MET cc_start: 0.6193 (mmp) cc_final: 0.5990 (mmm) REVERT: h 522 MET cc_start: 0.7352 (ppp) cc_final: 0.7130 (ppp) REVERT: l 10 MET cc_start: 0.8737 (mpp) cc_final: 0.8495 (mpp) REVERT: l 73 MET cc_start: 0.9352 (tpp) cc_final: 0.8379 (tpp) REVERT: l 77 MET cc_start: 0.9807 (mmp) cc_final: 0.9485 (mmp) REVERT: l 78 LYS cc_start: 0.9406 (mmpt) cc_final: 0.9191 (mmmt) REVERT: l 80 PHE cc_start: 0.9303 (m-80) cc_final: 0.9070 (m-80) REVERT: l 112 MET cc_start: 0.9843 (mmm) cc_final: 0.9603 (mmm) REVERT: l 130 MET cc_start: 0.9427 (mpp) cc_final: 0.9140 (tpt) REVERT: l 338 MET cc_start: 0.8867 (ppp) cc_final: 0.8594 (ppp) REVERT: l 466 MET cc_start: 0.9553 (ptt) cc_final: 0.8771 (ppp) REVERT: l 467 PHE cc_start: 0.9649 (m-80) cc_final: 0.9177 (m-80) REVERT: l 480 HIS cc_start: 0.9167 (m-70) cc_final: 0.8945 (m-70) REVERT: a 73 MET cc_start: 0.9394 (tpp) cc_final: 0.8238 (tpp) REVERT: a 77 MET cc_start: 0.9818 (mmp) cc_final: 0.9305 (mmm) REVERT: a 80 PHE cc_start: 0.9279 (m-80) cc_final: 0.8885 (m-80) REVERT: a 112 MET cc_start: 0.9797 (mmm) cc_final: 0.9275 (mmm) REVERT: a 338 MET cc_start: 0.9516 (ppp) cc_final: 0.9255 (ppp) REVERT: a 363 TYR cc_start: 0.9493 (m-80) cc_final: 0.9255 (m-80) REVERT: a 466 MET cc_start: 0.9203 (ppp) cc_final: 0.8971 (ppp) REVERT: a 467 PHE cc_start: 0.9104 (m-80) cc_final: 0.8732 (m-80) REVERT: a 476 PHE cc_start: 0.9403 (t80) cc_final: 0.8895 (t80) REVERT: a 517 VAL cc_start: 0.8254 (t) cc_final: 0.7472 (t) REVERT: b 73 MET cc_start: 0.9458 (tpt) cc_final: 0.8568 (tpp) REVERT: b 77 MET cc_start: 0.9517 (mmp) cc_final: 0.9296 (mmp) REVERT: b 112 MET cc_start: 0.9731 (mmm) cc_final: 0.9451 (mmm) REVERT: b 127 ASP cc_start: 0.8832 (m-30) cc_final: 0.8550 (m-30) REVERT: b 131 MET cc_start: 0.7868 (ttt) cc_final: 0.7655 (ttt) REVERT: b 467 PHE cc_start: 0.9210 (m-10) cc_final: 0.8821 (m-80) REVERT: b 480 HIS cc_start: 0.9479 (t70) cc_final: 0.9275 (t70) REVERT: b 534 ILE cc_start: 0.9539 (pt) cc_final: 0.9237 (pt) REVERT: b 537 MET cc_start: 0.9210 (ppp) cc_final: 0.9008 (ppp) REVERT: c 77 MET cc_start: 0.9717 (mmp) cc_final: 0.9253 (mmp) REVERT: c 130 MET cc_start: 0.9431 (tpt) cc_final: 0.8768 (tpt) REVERT: c 338 MET cc_start: 0.9401 (ppp) cc_final: 0.9133 (ppp) REVERT: d 73 MET cc_start: 0.9249 (tpp) cc_final: 0.7712 (tpp) REVERT: d 77 MET cc_start: 0.9620 (mmp) cc_final: 0.8973 (mmp) REVERT: d 338 MET cc_start: 0.8938 (ppp) cc_final: 0.8416 (ppp) REVERT: d 396 MET cc_start: 0.3897 (ttt) cc_final: 0.3678 (ttt) REVERT: d 466 MET cc_start: 0.9304 (ppp) cc_final: 0.8749 (ppp) REVERT: d 467 PHE cc_start: 0.9435 (m-10) cc_final: 0.9051 (m-80) REVERT: d 476 PHE cc_start: 0.9484 (t80) cc_final: 0.9191 (t80) REVERT: d 482 HIS cc_start: 0.8721 (m-70) cc_final: 0.8220 (p90) REVERT: e 77 MET cc_start: 0.9287 (mmp) cc_final: 0.9042 (mmm) REVERT: e 338 MET cc_start: 0.7833 (ppp) cc_final: 0.7304 (ppp) REVERT: e 447 MET cc_start: 0.7081 (pmm) cc_final: 0.6763 (ttt) outliers start: 3 outliers final: 0 residues processed: 439 average time/residue: 0.5700 time to fit residues: 421.6561 Evaluate side-chains 361 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 5.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 192 optimal weight: 6.9990 chunk 515 optimal weight: 40.0000 chunk 113 optimal weight: 20.0000 chunk 335 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 chunk 572 optimal weight: 20.0000 chunk 475 optimal weight: 30.0000 chunk 265 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 586 GLN ** j 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 530 HIS ** j 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 24 ASN i 480 HIS ** i 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 450 ASN ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 558 ASN ** a 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 506 ASN ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 450 ASN e 280 ASN ** e 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 366 ASN ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 49064 Z= 0.245 Angle : 0.730 9.916 66173 Z= 0.386 Chirality : 0.045 0.267 7239 Planarity : 0.005 0.066 8652 Dihedral : 5.460 31.355 6541 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 31.45 Ramachandran Plot: Outliers : 0.66 % Allowed : 19.61 % Favored : 79.72 % Rotamer: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.11), residues: 5869 helix: -0.50 (0.10), residues: 2587 sheet: -0.22 (0.28), residues: 442 loop : -3.93 (0.10), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP h 124 HIS 0.007 0.001 HIS k 482 PHE 0.041 0.002 PHE c 476 TYR 0.025 0.001 TYR h 106 ARG 0.014 0.001 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 431 time to evaluate : 6.129 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: 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: k 73 MET cc_start: 0.9717 (tpt) cc_final: 0.9004 (tpp) REVERT: k 77 MET cc_start: 0.9743 (mmp) cc_final: 0.9227 (mmm) REVERT: k 127 ASP cc_start: 0.9605 (m-30) cc_final: 0.9401 (m-30) REVERT: k 338 MET cc_start: 0.8563 (ppp) cc_final: 0.7842 (ppp) REVERT: k 466 MET cc_start: 0.9514 (ppp) cc_final: 0.9221 (ppp) REVERT: k 467 PHE cc_start: 0.9249 (m-80) cc_final: 0.8802 (m-80) REVERT: k 480 HIS cc_start: 0.9523 (t70) cc_final: 0.9212 (t70) REVERT: k 530 HIS cc_start: 0.9301 (m90) cc_final: 0.8843 (m-70) REVERT: k 537 MET cc_start: 0.9734 (ttp) cc_final: 0.9417 (mtp) REVERT: j 338 MET cc_start: 0.8007 (ppp) cc_final: 0.7634 (ppp) REVERT: j 467 PHE cc_start: 0.9531 (m-80) cc_final: 0.8878 (m-80) REVERT: j 480 HIS cc_start: 0.9525 (t70) cc_final: 0.9296 (t70) REVERT: j 580 ASN cc_start: 0.9210 (m110) cc_final: 0.8998 (m-40) REVERT: i 71 TRP cc_start: 0.8478 (m-90) cc_final: 0.8260 (m-90) REVERT: i 73 MET cc_start: 0.9685 (mmp) cc_final: 0.9467 (mmm) REVERT: i 112 MET cc_start: 0.9704 (mmt) cc_final: 0.9396 (mmt) REVERT: i 537 MET cc_start: 0.8329 (ptm) cc_final: 0.7843 (ppp) REVERT: l 10 MET cc_start: 0.8785 (mpp) cc_final: 0.8551 (mpp) REVERT: l 73 MET cc_start: 0.9372 (tpp) cc_final: 0.8488 (tpp) REVERT: l 77 MET cc_start: 0.9764 (mmp) cc_final: 0.9429 (mmp) REVERT: l 78 LYS cc_start: 0.9489 (mmpt) cc_final: 0.9226 (mmmt) REVERT: l 80 PHE cc_start: 0.9389 (m-80) cc_final: 0.8910 (m-80) REVERT: l 112 MET cc_start: 0.9826 (mmm) cc_final: 0.9524 (tpp) REVERT: l 127 ASP cc_start: 0.9161 (m-30) cc_final: 0.8910 (m-30) REVERT: l 130 MET cc_start: 0.9439 (mpp) cc_final: 0.9192 (tpt) REVERT: l 338 MET cc_start: 0.8999 (ppp) cc_final: 0.8695 (ppp) REVERT: l 466 MET cc_start: 0.9605 (ptt) cc_final: 0.8793 (ppp) REVERT: l 467 PHE cc_start: 0.9651 (m-80) cc_final: 0.9193 (m-80) REVERT: l 480 HIS cc_start: 0.9179 (m-70) cc_final: 0.8917 (m-70) REVERT: l 530 HIS cc_start: 0.9238 (m90) cc_final: 0.8870 (m-70) REVERT: l 537 MET cc_start: 0.9505 (ptm) cc_final: 0.9266 (ptm) REVERT: a 73 MET cc_start: 0.9403 (tpp) cc_final: 0.8383 (tpp) REVERT: a 77 MET cc_start: 0.9820 (mmp) cc_final: 0.9368 (mmp) REVERT: a 79 VAL cc_start: 0.9769 (m) cc_final: 0.9459 (p) REVERT: a 80 PHE cc_start: 0.9406 (m-80) cc_final: 0.8915 (m-80) REVERT: a 112 MET cc_start: 0.9789 (mmm) cc_final: 0.9236 (mmm) REVERT: a 338 MET cc_start: 0.9523 (ppp) cc_final: 0.9186 (ppp) REVERT: a 363 TYR cc_start: 0.9559 (m-80) cc_final: 0.9311 (m-80) REVERT: a 466 MET cc_start: 0.9310 (ppp) cc_final: 0.9051 (ppp) REVERT: a 467 PHE cc_start: 0.9197 (m-80) cc_final: 0.8878 (m-80) REVERT: a 480 HIS cc_start: 0.8818 (m-70) cc_final: 0.8377 (m-70) REVERT: b 73 MET cc_start: 0.9483 (tpt) cc_final: 0.8535 (tpp) REVERT: b 77 MET cc_start: 0.9489 (mmp) cc_final: 0.9083 (mmp) REVERT: b 466 MET cc_start: 0.9361 (ppp) cc_final: 0.9159 (ppp) REVERT: b 467 PHE cc_start: 0.9333 (m-10) cc_final: 0.8933 (m-80) REVERT: b 530 HIS cc_start: 0.9646 (m90) cc_final: 0.9322 (m90) REVERT: b 534 ILE cc_start: 0.9515 (pt) cc_final: 0.9255 (pt) REVERT: b 537 MET cc_start: 0.9252 (ppp) cc_final: 0.9037 (ppp) REVERT: c 77 MET cc_start: 0.9765 (mmp) cc_final: 0.9318 (mmp) REVERT: c 130 MET cc_start: 0.9446 (tpt) cc_final: 0.8820 (tpt) REVERT: c 338 MET cc_start: 0.9406 (ppp) cc_final: 0.9170 (ppp) REVERT: c 447 MET cc_start: 0.8055 (tpt) cc_final: 0.7853 (tmm) REVERT: d 73 MET cc_start: 0.9377 (tpp) cc_final: 0.8299 (tpp) REVERT: d 77 MET cc_start: 0.9631 (mmp) cc_final: 0.9312 (mmp) REVERT: d 338 MET cc_start: 0.8721 (ppp) cc_final: 0.8198 (ppp) REVERT: d 466 MET cc_start: 0.9310 (ppp) cc_final: 0.8819 (ppp) REVERT: d 467 PHE cc_start: 0.9459 (m-10) cc_final: 0.9125 (m-80) REVERT: d 476 PHE cc_start: 0.9414 (t80) cc_final: 0.9126 (t80) REVERT: d 482 HIS cc_start: 0.8623 (m-70) cc_final: 0.8327 (p90) REVERT: e 338 MET cc_start: 0.7667 (ppp) cc_final: 0.7080 (ppp) REVERT: e 447 MET cc_start: 0.7178 (pmm) cc_final: 0.6811 (ttt) outliers start: 1 outliers final: 1 residues processed: 432 average time/residue: 0.5747 time to fit residues: 416.5404 Evaluate side-chains 364 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 5.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 552 optimal weight: 50.0000 chunk 64 optimal weight: 50.0000 chunk 326 optimal weight: 1.9990 chunk 418 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 482 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 570 optimal weight: 10.0000 chunk 357 optimal weight: 30.0000 chunk 347 optimal weight: 0.8980 chunk 263 optimal weight: 30.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 450 ASN j 530 HIS i 480 HIS ** i 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 506 ASN ** l 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 506 ASN ** a 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 558 ASN ** b 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 49064 Z= 0.196 Angle : 0.725 10.859 66173 Z= 0.380 Chirality : 0.045 0.220 7239 Planarity : 0.005 0.080 8652 Dihedral : 5.448 31.355 6541 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 27.73 Ramachandran Plot: Outliers : 0.68 % Allowed : 19.58 % Favored : 79.74 % Rotamer: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.11), residues: 5869 helix: -0.52 (0.10), residues: 2595 sheet: -0.16 (0.28), residues: 442 loop : -3.90 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP g 499 HIS 0.007 0.001 HIS k 482 PHE 0.041 0.001 PHE c 476 TYR 0.020 0.001 TYR a 569 ARG 0.016 0.001 ARG j 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 441 time to evaluate : 5.381 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: 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: k 73 MET cc_start: 0.9741 (tpt) cc_final: 0.8975 (tpp) REVERT: k 77 MET cc_start: 0.9683 (mmp) cc_final: 0.9194 (mmm) REVERT: k 466 MET cc_start: 0.9518 (ppp) cc_final: 0.9186 (ppp) REVERT: k 467 PHE cc_start: 0.9295 (m-80) cc_final: 0.8962 (m-80) REVERT: k 480 HIS cc_start: 0.9472 (t70) cc_final: 0.9170 (t70) REVERT: k 530 HIS cc_start: 0.9286 (m90) cc_final: 0.8788 (m-70) REVERT: j 77 MET cc_start: 0.9752 (mmp) cc_final: 0.9511 (mmt) REVERT: j 131 MET cc_start: 0.7815 (tpt) cc_final: 0.7359 (tpt) REVERT: j 338 MET cc_start: 0.8041 (ppp) cc_final: 0.7704 (ppp) REVERT: j 467 PHE cc_start: 0.9531 (m-80) cc_final: 0.8867 (m-80) REVERT: j 480 HIS cc_start: 0.9523 (t70) cc_final: 0.9202 (t70) REVERT: j 580 ASN cc_start: 0.9167 (m110) cc_final: 0.8945 (m-40) REVERT: i 71 TRP cc_start: 0.8402 (m-90) cc_final: 0.8195 (m-90) REVERT: i 73 MET cc_start: 0.9705 (mmp) cc_final: 0.9463 (mmm) REVERT: i 112 MET cc_start: 0.9717 (mmt) cc_final: 0.9422 (mmm) REVERT: i 537 MET cc_start: 0.8471 (ptm) cc_final: 0.7991 (ppp) REVERT: h 522 MET cc_start: 0.7401 (ppp) cc_final: 0.7142 (ppp) REVERT: l 10 MET cc_start: 0.8724 (mpp) cc_final: 0.8504 (mpp) REVERT: l 73 MET cc_start: 0.9365 (tpp) cc_final: 0.8465 (tpp) REVERT: l 77 MET cc_start: 0.9743 (mmp) cc_final: 0.9378 (mmp) REVERT: l 78 LYS cc_start: 0.9373 (mmpt) cc_final: 0.9168 (mmmt) REVERT: l 80 PHE cc_start: 0.9357 (m-80) cc_final: 0.9056 (m-80) REVERT: l 112 MET cc_start: 0.9831 (mmm) cc_final: 0.9510 (tpp) REVERT: l 127 ASP cc_start: 0.9102 (m-30) cc_final: 0.8897 (m-30) REVERT: l 130 MET cc_start: 0.9496 (mpp) cc_final: 0.9187 (tpt) REVERT: l 338 MET cc_start: 0.8939 (ppp) cc_final: 0.8643 (ppp) REVERT: l 466 MET cc_start: 0.9602 (ptt) cc_final: 0.8780 (ppp) REVERT: l 467 PHE cc_start: 0.9634 (m-80) cc_final: 0.9192 (m-80) REVERT: l 480 HIS cc_start: 0.9223 (m-70) cc_final: 0.8893 (m-70) REVERT: l 530 HIS cc_start: 0.9218 (m90) cc_final: 0.8914 (m-70) REVERT: l 533 ARG cc_start: 0.9395 (mpp80) cc_final: 0.9163 (ptp-170) REVERT: l 537 MET cc_start: 0.9453 (ptm) cc_final: 0.9225 (ptm) REVERT: l 569 TYR cc_start: 0.9351 (m-10) cc_final: 0.9121 (m-10) REVERT: a 73 MET cc_start: 0.9400 (tpp) cc_final: 0.8341 (tpp) REVERT: a 77 MET cc_start: 0.9806 (mmp) cc_final: 0.9268 (mmp) REVERT: a 79 VAL cc_start: 0.9770 (m) cc_final: 0.9447 (p) REVERT: a 80 PHE cc_start: 0.9399 (m-80) cc_final: 0.8834 (m-80) REVERT: a 112 MET cc_start: 0.9796 (mmm) cc_final: 0.9495 (tpt) REVERT: a 338 MET cc_start: 0.9499 (ppp) cc_final: 0.9152 (ppp) REVERT: a 363 TYR cc_start: 0.9513 (m-80) cc_final: 0.9255 (m-80) REVERT: a 480 HIS cc_start: 0.8843 (m-70) cc_final: 0.8352 (m-70) REVERT: a 517 VAL cc_start: 0.8224 (t) cc_final: 0.7483 (t) REVERT: a 530 HIS cc_start: 0.9544 (m90) cc_final: 0.9334 (m90) REVERT: b 73 MET cc_start: 0.9465 (tpt) cc_final: 0.8387 (tpp) REVERT: b 77 MET cc_start: 0.9491 (mmp) cc_final: 0.8968 (mmp) REVERT: b 130 MET cc_start: 0.9324 (tpt) cc_final: 0.9073 (tpt) REVERT: b 466 MET cc_start: 0.9340 (ppp) cc_final: 0.9116 (ppp) REVERT: b 467 PHE cc_start: 0.9304 (m-10) cc_final: 0.8786 (m-80) REVERT: b 480 HIS cc_start: 0.9482 (t70) cc_final: 0.9245 (t70) REVERT: b 534 ILE cc_start: 0.9646 (pt) cc_final: 0.9208 (pt) REVERT: b 537 MET cc_start: 0.9272 (ppp) cc_final: 0.9043 (ppp) REVERT: c 77 MET cc_start: 0.9612 (mmp) cc_final: 0.9087 (mmp) REVERT: c 130 MET cc_start: 0.9437 (tpt) cc_final: 0.8820 (tpt) REVERT: c 338 MET cc_start: 0.9383 (ppp) cc_final: 0.9139 (ppp) REVERT: c 447 MET cc_start: 0.7989 (tpt) cc_final: 0.7732 (tmm) REVERT: d 73 MET cc_start: 0.9439 (tpp) cc_final: 0.8225 (tpp) REVERT: d 77 MET cc_start: 0.9687 (mmp) cc_final: 0.9220 (mmp) REVERT: d 338 MET cc_start: 0.8694 (ppp) cc_final: 0.8188 (ppp) REVERT: d 466 MET cc_start: 0.9338 (ppp) cc_final: 0.8796 (ppp) REVERT: d 467 PHE cc_start: 0.9432 (m-10) cc_final: 0.9108 (m-80) REVERT: d 482 HIS cc_start: 0.8720 (m-70) cc_final: 0.8258 (p90) REVERT: e 338 MET cc_start: 0.7722 (ppp) cc_final: 0.7160 (ppp) outliers start: 1 outliers final: 0 residues processed: 442 average time/residue: 0.5763 time to fit residues: 428.0513 Evaluate side-chains 372 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 6.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 353 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 340 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 362 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 282 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 448 optimal weight: 3.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 530 HIS i 480 HIS ** i 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 450 ASN ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 506 ASN ** l 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 450 ASN ** d 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 49064 Z= 0.195 Angle : 0.732 12.200 66173 Z= 0.381 Chirality : 0.045 0.206 7239 Planarity : 0.005 0.080 8652 Dihedral : 5.433 31.474 6541 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 27.41 Ramachandran Plot: Outliers : 0.68 % Allowed : 19.53 % Favored : 79.79 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.11), residues: 5869 helix: -0.49 (0.10), residues: 2605 sheet: -0.13 (0.28), residues: 442 loop : -3.93 (0.11), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP j 535 HIS 0.011 0.001 HIS d 530 PHE 0.041 0.001 PHE c 476 TYR 0.025 0.001 TYR c 363 ARG 0.011 0.000 ARG i 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 5.756 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: 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: k 73 MET cc_start: 0.9752 (tpt) cc_final: 0.8974 (tpp) REVERT: k 77 MET cc_start: 0.9665 (mmp) cc_final: 0.9194 (mmm) REVERT: k 466 MET cc_start: 0.9500 (ppp) cc_final: 0.9268 (ppp) REVERT: k 467 PHE cc_start: 0.9307 (m-80) cc_final: 0.8951 (m-80) REVERT: k 480 HIS cc_start: 0.9512 (t70) cc_final: 0.9227 (t70) REVERT: k 530 HIS cc_start: 0.9278 (m90) cc_final: 0.8736 (m-70) REVERT: j 77 MET cc_start: 0.9720 (mmp) cc_final: 0.9362 (mmt) REVERT: j 131 MET cc_start: 0.8163 (tpt) cc_final: 0.7767 (tpt) REVERT: j 338 MET cc_start: 0.8044 (ppp) cc_final: 0.7728 (ppp) REVERT: j 467 PHE cc_start: 0.9542 (m-80) cc_final: 0.8876 (m-80) REVERT: j 480 HIS cc_start: 0.9502 (t70) cc_final: 0.9182 (t70) REVERT: j 486 TYR cc_start: 0.8679 (t80) cc_final: 0.7368 (t80) REVERT: j 537 MET cc_start: 0.9619 (mpp) cc_final: 0.9398 (mpp) REVERT: i 112 MET cc_start: 0.9703 (mmt) cc_final: 0.9408 (mmm) REVERT: i 537 MET cc_start: 0.8523 (ptm) cc_final: 0.8030 (ppp) REVERT: h 522 MET cc_start: 0.7446 (ppp) cc_final: 0.7174 (ppp) REVERT: l 10 MET cc_start: 0.8718 (mpp) cc_final: 0.8499 (mpp) REVERT: l 73 MET cc_start: 0.9377 (tpp) cc_final: 0.8465 (tpp) REVERT: l 77 MET cc_start: 0.9744 (mmp) cc_final: 0.9369 (mmp) REVERT: l 78 LYS cc_start: 0.9476 (mmpt) cc_final: 0.9173 (mmmt) REVERT: l 112 MET cc_start: 0.9827 (mmm) cc_final: 0.9486 (tpp) REVERT: l 130 MET cc_start: 0.9502 (mpp) cc_final: 0.9186 (tpt) REVERT: l 338 MET cc_start: 0.8964 (ppp) cc_final: 0.8675 (ppp) REVERT: l 466 MET cc_start: 0.9618 (ptt) cc_final: 0.8787 (ppp) REVERT: l 467 PHE cc_start: 0.9642 (m-80) cc_final: 0.9215 (m-80) REVERT: l 480 HIS cc_start: 0.9236 (m-70) cc_final: 0.8948 (m-70) REVERT: l 530 HIS cc_start: 0.9225 (m90) cc_final: 0.8917 (m-70) REVERT: l 533 ARG cc_start: 0.9393 (mpp80) cc_final: 0.9147 (ptp-170) REVERT: l 569 TYR cc_start: 0.9358 (m-10) cc_final: 0.9141 (m-10) REVERT: a 73 MET cc_start: 0.9406 (tpp) cc_final: 0.8341 (tpp) REVERT: a 77 MET cc_start: 0.9815 (mmp) cc_final: 0.9259 (mmp) REVERT: a 79 VAL cc_start: 0.9787 (m) cc_final: 0.9464 (p) REVERT: a 80 PHE cc_start: 0.9432 (m-80) cc_final: 0.8859 (m-80) REVERT: a 112 MET cc_start: 0.9794 (mmm) cc_final: 0.9191 (mmm) REVERT: a 329 TYR cc_start: 0.8607 (m-80) cc_final: 0.7766 (m-80) REVERT: a 338 MET cc_start: 0.9581 (ppp) cc_final: 0.9158 (ppp) REVERT: a 363 TYR cc_start: 0.9600 (m-80) cc_final: 0.9392 (m-80) REVERT: a 480 HIS cc_start: 0.8882 (m-70) cc_final: 0.8476 (m-70) REVERT: a 517 VAL cc_start: 0.8294 (t) cc_final: 0.7505 (t) REVERT: a 530 HIS cc_start: 0.9540 (m90) cc_final: 0.9324 (m90) REVERT: b 73 MET cc_start: 0.9461 (tpt) cc_final: 0.8280 (tpp) REVERT: b 77 MET cc_start: 0.9470 (mmp) cc_final: 0.8886 (mmp) REVERT: b 112 MET cc_start: 0.9827 (mmm) cc_final: 0.8897 (mmm) REVERT: b 127 ASP cc_start: 0.8819 (m-30) cc_final: 0.8499 (m-30) REVERT: b 130 MET cc_start: 0.9319 (tpt) cc_final: 0.9074 (tpt) REVERT: b 466 MET cc_start: 0.9322 (ppp) cc_final: 0.9105 (ppp) REVERT: b 467 PHE cc_start: 0.9317 (m-10) cc_final: 0.8790 (m-80) REVERT: b 480 HIS cc_start: 0.9471 (t70) cc_final: 0.9240 (t70) REVERT: b 534 ILE cc_start: 0.9645 (pt) cc_final: 0.9127 (pt) REVERT: b 537 MET cc_start: 0.9278 (ppp) cc_final: 0.9027 (ppp) REVERT: c 77 MET cc_start: 0.9597 (mmp) cc_final: 0.9082 (mmp) REVERT: c 130 MET cc_start: 0.9445 (tpt) cc_final: 0.8832 (tpt) REVERT: c 338 MET cc_start: 0.9381 (ppp) cc_final: 0.9159 (ppp) REVERT: c 447 MET cc_start: 0.7960 (tpt) cc_final: 0.7750 (tmm) REVERT: c 524 LYS cc_start: 0.9475 (tppt) cc_final: 0.9084 (tppt) REVERT: d 73 MET cc_start: 0.9403 (tpp) cc_final: 0.8229 (tpp) REVERT: d 77 MET cc_start: 0.9659 (mmp) cc_final: 0.9289 (mmp) REVERT: d 112 MET cc_start: 0.9703 (mmm) cc_final: 0.9203 (mmm) REVERT: d 338 MET cc_start: 0.8716 (ppp) cc_final: 0.8220 (ppp) REVERT: d 466 MET cc_start: 0.9464 (ppp) cc_final: 0.9187 (ppp) REVERT: d 467 PHE cc_start: 0.9415 (m-10) cc_final: 0.9071 (m-80) REVERT: d 482 HIS cc_start: 0.8698 (m-70) cc_final: 0.8175 (p90) REVERT: d 537 MET cc_start: 0.9667 (pmm) cc_final: 0.9300 (pmm) REVERT: e 338 MET cc_start: 0.7719 (ppp) cc_final: 0.7099 (ppp) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.5841 time to fit residues: 434.1528 Evaluate side-chains 373 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 4.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 519 optimal weight: 50.0000 chunk 546 optimal weight: 30.0000 chunk 498 optimal weight: 9.9990 chunk 531 optimal weight: 8.9990 chunk 320 optimal weight: 20.0000 chunk 231 optimal weight: 7.9990 chunk 417 optimal weight: 7.9990 chunk 163 optimal weight: 30.0000 chunk 480 optimal weight: 6.9990 chunk 502 optimal weight: 8.9990 chunk 529 optimal weight: 50.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 530 HIS ** j 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 480 HIS ** i 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 521 ASN ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 333 HIS ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 558 ASN ** a 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 49064 Z= 0.261 Angle : 0.769 11.632 66173 Z= 0.405 Chirality : 0.046 0.245 7239 Planarity : 0.006 0.086 8652 Dihedral : 5.570 31.745 6541 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 34.20 Ramachandran Plot: Outliers : 0.68 % Allowed : 19.99 % Favored : 79.33 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.11), residues: 5869 helix: -0.55 (0.10), residues: 2594 sheet: -0.32 (0.28), residues: 442 loop : -3.96 (0.10), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP i 71 HIS 0.009 0.001 HIS l 482 PHE 0.040 0.002 PHE c 476 TYR 0.019 0.002 TYR b 363 ARG 0.011 0.001 ARG i 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 4.893 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: 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: k 73 MET cc_start: 0.9752 (tpt) cc_final: 0.8981 (tpp) REVERT: k 77 MET cc_start: 0.9751 (mmp) cc_final: 0.9321 (mmm) REVERT: k 466 MET cc_start: 0.9490 (ppp) cc_final: 0.9206 (ppp) REVERT: k 467 PHE cc_start: 0.9341 (m-80) cc_final: 0.8895 (m-80) REVERT: k 480 HIS cc_start: 0.9551 (t70) cc_final: 0.9283 (t70) REVERT: k 522 MET cc_start: 0.9340 (ppp) cc_final: 0.9130 (ppp) REVERT: k 530 HIS cc_start: 0.9331 (m90) cc_final: 0.8827 (m90) REVERT: j 338 MET cc_start: 0.8172 (ppp) cc_final: 0.7819 (ppp) REVERT: j 467 PHE cc_start: 0.9577 (m-80) cc_final: 0.8943 (m-80) REVERT: j 480 HIS cc_start: 0.9501 (t70) cc_final: 0.9295 (t70) REVERT: j 486 TYR cc_start: 0.8826 (t80) cc_final: 0.7640 (t80) REVERT: i 73 MET cc_start: 0.9639 (mmp) cc_final: 0.9392 (mmm) REVERT: i 112 MET cc_start: 0.9699 (mmt) cc_final: 0.9361 (mmm) REVERT: i 537 MET cc_start: 0.8682 (ptm) cc_final: 0.8185 (ppp) REVERT: l 73 MET cc_start: 0.9401 (tpp) cc_final: 0.8569 (tpp) REVERT: l 77 MET cc_start: 0.9741 (mmp) cc_final: 0.9421 (mmp) REVERT: l 112 MET cc_start: 0.9799 (mmm) cc_final: 0.9540 (mmm) REVERT: l 127 ASP cc_start: 0.9197 (m-30) cc_final: 0.8950 (m-30) REVERT: l 130 MET cc_start: 0.9541 (mpp) cc_final: 0.9226 (tpt) REVERT: l 338 MET cc_start: 0.9128 (ppp) cc_final: 0.8838 (ppp) REVERT: l 466 MET cc_start: 0.9690 (ptt) cc_final: 0.8919 (ppp) REVERT: l 467 PHE cc_start: 0.9649 (m-80) cc_final: 0.9249 (m-80) REVERT: l 530 HIS cc_start: 0.9263 (m90) cc_final: 0.8860 (m-70) REVERT: a 73 MET cc_start: 0.9412 (tpp) cc_final: 0.8400 (tpp) REVERT: a 77 MET cc_start: 0.9859 (mmp) cc_final: 0.9282 (mmp) REVERT: a 112 MET cc_start: 0.9765 (mmm) cc_final: 0.9016 (mmm) REVERT: a 338 MET cc_start: 0.9484 (ppp) cc_final: 0.9094 (ppp) REVERT: a 363 TYR cc_start: 0.9487 (m-80) cc_final: 0.9249 (m-80) REVERT: a 466 MET cc_start: 0.9239 (ppp) cc_final: 0.9031 (ppp) REVERT: a 467 PHE cc_start: 0.9244 (m-80) cc_final: 0.8981 (m-80) REVERT: a 480 HIS cc_start: 0.8908 (m-70) cc_final: 0.8544 (m-70) REVERT: b 73 MET cc_start: 0.9444 (tpt) cc_final: 0.8467 (tpp) REVERT: b 77 MET cc_start: 0.9473 (mmp) cc_final: 0.9043 (mmp) REVERT: b 127 ASP cc_start: 0.8950 (m-30) cc_final: 0.8465 (t0) REVERT: b 130 MET cc_start: 0.9364 (tpt) cc_final: 0.9129 (tpt) REVERT: b 131 MET cc_start: 0.7964 (ttt) cc_final: 0.7234 (ttt) REVERT: b 467 PHE cc_start: 0.9292 (m-10) cc_final: 0.8934 (m-80) REVERT: b 480 HIS cc_start: 0.9509 (t70) cc_final: 0.9303 (t70) REVERT: b 534 ILE cc_start: 0.9506 (pt) cc_final: 0.9257 (pt) REVERT: b 537 MET cc_start: 0.9355 (ppp) cc_final: 0.9090 (ppp) REVERT: c 77 MET cc_start: 0.9656 (mmp) cc_final: 0.9137 (mmp) REVERT: c 130 MET cc_start: 0.9446 (tpt) cc_final: 0.8837 (tpt) REVERT: c 447 MET cc_start: 0.8025 (tpt) cc_final: 0.7805 (tmm) REVERT: c 482 HIS cc_start: 0.8326 (m90) cc_final: 0.8012 (m-70) REVERT: d 73 MET cc_start: 0.9518 (tpp) cc_final: 0.8399 (tpp) REVERT: d 77 MET cc_start: 0.9685 (mmp) cc_final: 0.9127 (mmp) REVERT: d 338 MET cc_start: 0.8791 (ppp) cc_final: 0.8358 (ppp) REVERT: d 466 MET cc_start: 0.9553 (ppp) cc_final: 0.9295 (ppp) REVERT: d 467 PHE cc_start: 0.9435 (m-10) cc_final: 0.9045 (m-80) REVERT: d 482 HIS cc_start: 0.8690 (m-70) cc_final: 0.8338 (p90) REVERT: e 77 MET cc_start: 0.9480 (mmp) cc_final: 0.9148 (mmm) REVERT: e 338 MET cc_start: 0.8184 (ppp) cc_final: 0.7670 (ppp) REVERT: e 463 ILE cc_start: 0.9027 (mp) cc_final: 0.8636 (mm) REVERT: f 462 LEU cc_start: 0.9122 (mp) cc_final: 0.8754 (mp) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.5848 time to fit residues: 425.2913 Evaluate side-chains 366 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 5.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 349 optimal weight: 3.9990 chunk 562 optimal weight: 0.2980 chunk 343 optimal weight: 20.0000 chunk 266 optimal weight: 8.9990 chunk 390 optimal weight: 8.9990 chunk 589 optimal weight: 20.0000 chunk 542 optimal weight: 8.9990 chunk 469 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 287 optimal weight: 6.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 530 HIS j 554 GLN ** j 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 480 HIS ** i 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 506 ASN ** l 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 558 ASN ** b 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 450 ASN ** e 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 14 GLN ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 49064 Z= 0.213 Angle : 0.769 12.490 66173 Z= 0.402 Chirality : 0.046 0.285 7239 Planarity : 0.005 0.084 8652 Dihedral : 5.542 31.578 6541 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 29.78 Ramachandran Plot: Outliers : 0.70 % Allowed : 19.49 % Favored : 79.81 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.11), residues: 5869 helix: -0.52 (0.10), residues: 2592 sheet: -0.25 (0.28), residues: 442 loop : -3.96 (0.10), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.002 TRP h 124 HIS 0.007 0.001 HIS k 482 PHE 0.038 0.001 PHE c 476 TYR 0.024 0.001 TYR a 569 ARG 0.012 0.001 ARG l 422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11738 Ramachandran restraints generated. 5869 Oldfield, 0 Emsley, 5869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 5.250 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 73 MET cc_start: 0.9760 (tpt) cc_final: 0.8988 (tpp) REVERT: k 77 MET cc_start: 0.9711 (mmp) cc_final: 0.9183 (mmm) REVERT: k 127 ASP cc_start: 0.9451 (m-30) cc_final: 0.8882 (t0) REVERT: k 466 MET cc_start: 0.9465 (ppp) cc_final: 0.9148 (ppp) REVERT: k 467 PHE cc_start: 0.9398 (m-80) cc_final: 0.9038 (m-80) REVERT: k 480 HIS cc_start: 0.9520 (t70) cc_final: 0.9248 (t70) REVERT: k 530 HIS cc_start: 0.9353 (m90) cc_final: 0.8794 (m-70) REVERT: j 131 MET cc_start: 0.8395 (tpt) cc_final: 0.7880 (tpt) REVERT: j 338 MET cc_start: 0.8144 (ppp) cc_final: 0.7825 (ppp) REVERT: j 467 PHE cc_start: 0.9566 (m-80) cc_final: 0.8916 (m-80) REVERT: j 480 HIS cc_start: 0.9448 (t70) cc_final: 0.9185 (t70) REVERT: j 486 TYR cc_start: 0.8857 (t80) cc_final: 0.7531 (t80) REVERT: j 537 MET cc_start: 0.9642 (mpp) cc_final: 0.9440 (mpp) REVERT: i 73 MET cc_start: 0.9650 (mmp) cc_final: 0.9364 (mmm) REVERT: i 112 MET cc_start: 0.9679 (mmt) cc_final: 0.9373 (mmm) REVERT: i 537 MET cc_start: 0.8702 (ptm) cc_final: 0.8203 (ppp) REVERT: h 522 MET cc_start: 0.7383 (ppp) cc_final: 0.7076 (ppp) REVERT: l 73 MET cc_start: 0.9389 (tpp) cc_final: 0.8514 (tpp) REVERT: l 77 MET cc_start: 0.9756 (mmp) cc_final: 0.9412 (mmp) REVERT: l 78 LYS cc_start: 0.9510 (mtmm) cc_final: 0.9284 (ptpt) REVERT: l 112 MET cc_start: 0.9805 (mmm) cc_final: 0.9461 (mmm) REVERT: l 127 ASP cc_start: 0.9172 (m-30) cc_final: 0.8965 (m-30) REVERT: l 130 MET cc_start: 0.9529 (mpp) cc_final: 0.9219 (tpt) REVERT: l 338 MET cc_start: 0.9058 (ppp) cc_final: 0.8838 (ppp) REVERT: l 466 MET cc_start: 0.9678 (ptt) cc_final: 0.8909 (ppp) REVERT: l 467 PHE cc_start: 0.9626 (m-80) cc_final: 0.9245 (m-80) REVERT: l 480 HIS cc_start: 0.9239 (m-70) cc_final: 0.8910 (m-70) REVERT: l 530 HIS cc_start: 0.9269 (m90) cc_final: 0.8893 (m90) REVERT: l 533 ARG cc_start: 0.9417 (mpp80) cc_final: 0.9107 (ptt180) REVERT: l 569 TYR cc_start: 0.9404 (m-10) cc_final: 0.9149 (m-10) REVERT: a 73 MET cc_start: 0.9406 (tpp) cc_final: 0.8366 (tpp) REVERT: a 77 MET cc_start: 0.9842 (mmp) cc_final: 0.9258 (mmp) REVERT: a 112 MET cc_start: 0.9752 (mmm) cc_final: 0.9221 (mmm) REVERT: a 338 MET cc_start: 0.9466 (ppp) cc_final: 0.9054 (ppp) REVERT: a 363 TYR cc_start: 0.9498 (m-80) cc_final: 0.9276 (m-80) REVERT: a 480 HIS cc_start: 0.8893 (m-70) cc_final: 0.8524 (m-70) REVERT: a 569 TYR cc_start: 0.7983 (p90) cc_final: 0.7625 (p90) REVERT: b 73 MET cc_start: 0.9440 (tpt) cc_final: 0.8456 (tpp) REVERT: b 77 MET cc_start: 0.9427 (mmp) cc_final: 0.8985 (mmp) REVERT: b 112 MET cc_start: 0.9811 (mmm) cc_final: 0.8928 (mmm) REVERT: b 127 ASP cc_start: 0.8901 (m-30) cc_final: 0.8266 (t0) REVERT: b 130 MET cc_start: 0.9321 (tpt) cc_final: 0.9081 (tpt) REVERT: b 131 MET cc_start: 0.7885 (ttt) cc_final: 0.6955 (ttt) REVERT: b 467 PHE cc_start: 0.9297 (m-10) cc_final: 0.8815 (m-80) REVERT: b 480 HIS cc_start: 0.9488 (t70) cc_final: 0.9284 (t70) REVERT: b 534 ILE cc_start: 0.9661 (pt) cc_final: 0.9232 (pt) REVERT: b 537 MET cc_start: 0.9302 (ppp) cc_final: 0.9046 (ppp) REVERT: c 77 MET cc_start: 0.9615 (mmp) cc_final: 0.9097 (mmp) REVERT: c 130 MET cc_start: 0.9459 (tpt) cc_final: 0.8868 (tpt) REVERT: c 338 MET cc_start: 0.9449 (ppp) cc_final: 0.9116 (ppp) REVERT: c 447 MET cc_start: 0.8043 (tpt) cc_final: 0.7809 (tmm) REVERT: c 482 HIS cc_start: 0.8301 (m90) cc_final: 0.7975 (m-70) REVERT: d 73 MET cc_start: 0.9419 (tpp) cc_final: 0.8303 (tpp) REVERT: d 77 MET cc_start: 0.9568 (mmp) cc_final: 0.9264 (mmp) REVERT: d 112 MET cc_start: 0.9704 (mmm) cc_final: 0.9153 (mmm) REVERT: d 338 MET cc_start: 0.8770 (ppp) cc_final: 0.8310 (ppp) REVERT: d 466 MET cc_start: 0.9592 (ppp) cc_final: 0.9343 (ppp) REVERT: d 480 HIS cc_start: 0.9552 (t70) cc_final: 0.9345 (t70) REVERT: d 482 HIS cc_start: 0.8756 (m-70) cc_final: 0.8268 (p90) REVERT: d 537 MET cc_start: 0.9668 (pmm) cc_final: 0.9292 (pmm) REVERT: e 77 MET cc_start: 0.9299 (mmp) cc_final: 0.8992 (mmm) REVERT: e 130 MET cc_start: 0.9495 (mpp) cc_final: 0.7912 (tpt) REVERT: e 338 MET cc_start: 0.8342 (ppp) cc_final: 0.7874 (ppp) REVERT: f 462 LEU cc_start: 0.9094 (mp) cc_final: 0.8685 (mp) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.5784 time to fit residues: 423.6237 Evaluate side-chains 369 residues out of total 5263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 5.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 373 optimal weight: 30.0000 chunk 500 optimal weight: 40.0000 chunk 143 optimal weight: 9.9990 chunk 433 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 470 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 483 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 86 optimal weight: 30.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 530 HIS ** j 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 480 HIS ** i 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 593 GLN ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 558 ASN ** a 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.090142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.067209 restraints weight = 510535.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.067866 restraints weight = 346435.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.068318 restraints weight = 257037.958| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 49064 Z= 0.267 Angle : 0.792 11.531 66173 Z= 0.418 Chirality : 0.047 0.268 7239 Planarity : 0.006 0.088 8652 Dihedral : 5.681 32.221 6541 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 35.03 Ramachandran Plot: Outliers : 0.68 % Allowed : 20.28 % Favored : 79.04 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.11), residues: 5869 helix: -0.58 (0.10), residues: 2588 sheet: -0.43 (0.27), residues: 442 loop : -3.98 (0.10), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP h 124 HIS 0.010 0.001 HIS l 482 PHE 0.039 0.002 PHE c 476 TYR 0.044 0.002 TYR c 412 ARG 0.012 0.001 ARG l 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8823.74 seconds wall clock time: 162 minutes 22.16 seconds (9742.16 seconds total)