Starting phenix.real_space_refine on Thu Feb 22 03:58:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkg_16097/02_2024/8bkg_16097.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkg_16097/02_2024/8bkg_16097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkg_16097/02_2024/8bkg_16097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkg_16097/02_2024/8bkg_16097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkg_16097/02_2024/8bkg_16097.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkg_16097/02_2024/8bkg_16097.pdb" } resolution = 3.2 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= 0.012 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 156 5.16 5 C 20760 2.51 5 N 5808 2.21 5 O 6100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ASP 859": "OD1" <-> "OD2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B ASP 492": "OD1" <-> "OD2" Residue "B ASP 509": "OD1" <-> "OD2" Residue "B TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ASP 859": "OD1" <-> "OD2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C ASP 492": "OD1" <-> "OD2" Residue "C ASP 509": "OD1" <-> "OD2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 684": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C ASP 859": "OD1" <-> "OD2" Residue "C GLU 904": "OE1" <-> "OE2" Residue "C PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D ASP 492": "OD1" <-> "OD2" Residue "D ASP 509": "OD1" <-> "OD2" Residue "D TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 684": "OE1" <-> "OE2" Residue "D GLU 819": "OE1" <-> "OE2" Residue "D ASP 859": "OD1" <-> "OD2" Residue "D GLU 904": "OE1" <-> "OE2" Residue "D PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32824 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 58, 'TRANS': 958} Chain: "B" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 58, 'TRANS': 958} Chain: "C" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 58, 'TRANS': 958} Chain: "D" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 58, 'TRANS': 958} Time building chain proxies: 17.16, per 1000 atoms: 0.52 Number of scatterers: 32824 At special positions: 0 Unit cell: (194.79, 152.51, 104.19, 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 156 16.00 O 6100 8.00 N 5808 7.00 C 20760 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: 12.57 Conformation dependent library (CDL) restraints added in 6.1 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7608 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 52 sheets defined 17.9% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.584A pdb=" N VAL A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 13 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.790A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.745A pdb=" N HIS A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 4.007A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.809A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 465 through 479 Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.565A pdb=" N GLY A 490 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 491 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP A 492 " --> pdb=" O GLY A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 492' Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.860A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.136A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 813 Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.736A pdb=" N TYR A 926 " --> pdb=" O SER A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.523A pdb=" N GLN A1008 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 removed outlier: 3.584A pdb=" N VAL B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 13 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.790A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.745A pdb=" N HIS B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.007A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.809A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 440 through 447 Processing helix chain 'B' and resid 465 through 479 Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.565A pdb=" N GLY B 490 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 491 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP B 492 " --> pdb=" O GLY B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.860A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 4.136A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 813 Processing helix chain 'B' and resid 923 through 926 removed outlier: 3.736A pdb=" N TYR B 926 " --> pdb=" O SER B 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.523A pdb=" N GLN B1008 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 removed outlier: 3.584A pdb=" N VAL C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.790A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.745A pdb=" N HIS C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 4.007A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.809A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 440 through 447 Processing helix chain 'C' and resid 465 through 479 Processing helix chain 'C' and resid 487 through 492 removed outlier: 3.565A pdb=" N GLY C 490 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 491 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP C 492 " --> pdb=" O GLY C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 492' Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.860A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 624 removed outlier: 4.136A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 923 through 926 removed outlier: 3.736A pdb=" N TYR C 926 " --> pdb=" O SER C 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 1004 through 1008 removed outlier: 3.523A pdb=" N GLN C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 13 removed outlier: 3.584A pdb=" N VAL D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.790A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.745A pdb=" N HIS D 93 " --> pdb=" O ASN D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 136 removed outlier: 4.007A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.809A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 440 through 447 Processing helix chain 'D' and resid 465 through 479 Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.565A pdb=" N GLY D 490 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 491 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP D 492 " --> pdb=" O GLY D 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 487 through 492' Processing helix chain 'D' and resid 519 through 525 Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 599 through 603 removed outlier: 3.860A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.136A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 813 Processing helix chain 'D' and resid 923 through 926 removed outlier: 3.736A pdb=" N TYR D 926 " --> pdb=" O SER D 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 1004 through 1008 removed outlier: 3.523A pdb=" N GLN D1008 " --> pdb=" O ALA D1005 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 86 removed outlier: 8.773A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 129 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.168A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.662A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.873A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485 removed outlier: 7.910A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TRP A 568 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N GLU A 537 " --> pdb=" O TRP A 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 669 removed outlier: 5.866A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 664 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.139A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.547A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.352A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY A 940 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 900 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 898 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 944 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN A 896 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR A 946 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ARG A 894 " --> pdb=" O TYR A 946 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 86 removed outlier: 8.773A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 129 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.168A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.662A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.873A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC2, first strand: chain 'B' and resid 484 through 485 removed outlier: 7.910A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TRP B 568 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N GLU B 537 " --> pdb=" O TRP B 568 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC4, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC5, first strand: chain 'B' and resid 661 through 669 removed outlier: 5.866A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 664 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.139A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.547A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.352A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY B 940 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 900 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 898 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 944 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN B 896 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR B 946 " --> pdb=" O ARG B 894 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ARG B 894 " --> pdb=" O TYR B 946 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD1, first strand: chain 'C' and resid 82 through 86 removed outlier: 8.773A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 129 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 99 through 101 removed outlier: 4.168A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.662A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.873A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD6, first strand: chain 'C' and resid 484 through 485 removed outlier: 7.910A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TRP C 568 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N GLU C 537 " --> pdb=" O TRP C 568 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AD8, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD9, first strand: chain 'C' and resid 661 through 669 removed outlier: 5.866A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 664 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.139A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.547A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.352A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY C 940 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 900 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 898 " --> pdb=" O ARG C 942 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 944 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 896 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR C 946 " --> pdb=" O ARG C 894 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ARG C 894 " --> pdb=" O TYR C 946 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE5, first strand: chain 'D' and resid 82 through 86 removed outlier: 8.773A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 129 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.168A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.662A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.873A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF1, first strand: chain 'D' and resid 484 through 485 removed outlier: 7.910A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TRP D 568 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N GLU D 537 " --> pdb=" O TRP D 568 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF3, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF4, first strand: chain 'D' and resid 661 through 669 removed outlier: 5.866A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 664 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.139A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.547A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.352A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY D 940 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 900 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU D 898 " --> pdb=" O ARG D 942 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU D 944 " --> pdb=" O ASN D 896 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN D 896 " --> pdb=" O LEU D 944 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR D 946 " --> pdb=" O ARG D 894 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ARG D 894 " --> pdb=" O TYR D 946 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3144 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: 13.62 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: 11072 1.34 - 1.46: 8220 1.46 - 1.58: 14252 1.58 - 1.70: 0 1.70 - 1.82: 248 Bond restraints: 33792 Sorted by residual: bond pdb=" C THR C 595 " pdb=" N PRO C 596 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.04e+00 bond pdb=" C THR D 595 " pdb=" N PRO D 596 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.04e+00 bond pdb=" C THR B 595 " pdb=" N PRO B 596 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.04e+00 bond pdb=" C THR A 595 " pdb=" N PRO A 596 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.04e+00 bond pdb=" CA ASN C 958 " pdb=" CB ASN C 958 " ideal model delta sigma weight residual 1.534 1.556 -0.023 1.72e-02 3.38e+03 1.74e+00 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.66: 872 105.66 - 112.83: 17684 112.83 - 120.00: 11612 120.00 - 127.17: 15244 127.17 - 134.34: 692 Bond angle restraints: 46104 Sorted by residual: angle pdb=" N GLY A 488 " pdb=" CA GLY A 488 " pdb=" C GLY A 488 " ideal model delta sigma weight residual 111.36 116.19 -4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" N GLY D 488 " pdb=" CA GLY D 488 " pdb=" C GLY D 488 " ideal model delta sigma weight residual 111.36 116.19 -4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" N GLY B 488 " pdb=" CA GLY B 488 " pdb=" C GLY B 488 " ideal model delta sigma weight residual 111.36 116.19 -4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" N GLY C 488 " pdb=" CA GLY C 488 " pdb=" C GLY C 488 " ideal model delta sigma weight residual 111.36 116.19 -4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" CB MET D 745 " pdb=" CG MET D 745 " pdb=" SD MET D 745 " ideal model delta sigma weight residual 112.70 125.04 -12.34 3.00e+00 1.11e-01 1.69e+01 ... (remaining 46099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 17424 17.20 - 34.40: 1800 34.40 - 51.60: 432 51.60 - 68.81: 100 68.81 - 86.01: 44 Dihedral angle restraints: 19800 sinusoidal: 7984 harmonic: 11816 Sorted by residual: dihedral pdb=" CA GLU B 580 " pdb=" C GLU B 580 " pdb=" N ASN B 581 " pdb=" CA ASN B 581 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU D 580 " pdb=" C GLU D 580 " pdb=" N ASN D 581 " pdb=" CA ASN D 581 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU A 580 " pdb=" C GLU A 580 " pdb=" N ASN A 581 " pdb=" CA ASN A 581 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 19797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3252 0.037 - 0.073: 1100 0.073 - 0.110: 348 0.110 - 0.147: 112 0.147 - 0.183: 8 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CA THR C 595 " pdb=" N THR C 595 " pdb=" C THR C 595 " pdb=" CB THR C 595 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA THR A 595 " pdb=" N THR A 595 " pdb=" C THR A 595 " pdb=" CB THR A 595 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA THR D 595 " pdb=" N THR D 595 " pdb=" C THR D 595 " pdb=" CB THR D 595 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 4817 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 906 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO C 907 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 907 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 907 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 906 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 907 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 907 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 907 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 906 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO D 907 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 907 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 907 " 0.027 5.00e-02 4.00e+02 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5438 2.77 - 3.30: 28330 3.30 - 3.84: 57982 3.84 - 4.37: 69062 4.37 - 4.90: 120642 Nonbonded interactions: 281454 Sorted by model distance: nonbonded pdb=" O ASP A 594 " pdb=" ND2 ASN A 597 " model vdw 2.241 2.520 nonbonded pdb=" O ASP D 594 " pdb=" ND2 ASN D 597 " model vdw 2.241 2.520 nonbonded pdb=" O ASP C 594 " pdb=" ND2 ASN C 597 " model vdw 2.241 2.520 nonbonded pdb=" O ASP B 594 " pdb=" ND2 ASN B 597 " model vdw 2.241 2.520 nonbonded pdb=" O PRO D 434 " pdb=" OG SER D 437 " model vdw 2.248 2.440 ... (remaining 281449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.600 Check model and map are aligned: 0.510 Set scattering table: 0.320 Process input model: 87.110 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.180 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 0.049 33792 Z= 0.184 Angle : 0.572 12.342 46104 Z= 0.310 Chirality : 0.043 0.183 4820 Planarity : 0.004 0.049 6088 Dihedral : 15.302 86.007 12192 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.57 % Allowed : 16.36 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 4080 helix: -0.76 (0.21), residues: 540 sheet: 0.47 (0.14), residues: 1352 loop : -0.48 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 90 HIS 0.009 0.001 HIS B 391 PHE 0.007 0.001 PHE A 274 TYR 0.014 0.001 TYR B1016 ARG 0.005 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 4.212 Fit side-chains outliers start: 20 outliers final: 20 residues processed: 228 average time/residue: 0.4695 time to fit residues: 174.4851 Evaluate side-chains 220 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 837 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 9.9990 chunk 309 optimal weight: 0.0050 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 319 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 9.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 93 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 HIS C 93 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS D 93 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 33792 Z= 0.371 Angle : 0.584 9.919 46104 Z= 0.302 Chirality : 0.046 0.149 4820 Planarity : 0.005 0.042 6088 Dihedral : 4.935 45.691 4496 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 2.17 % Allowed : 14.53 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4080 helix: -0.40 (0.22), residues: 524 sheet: 0.32 (0.14), residues: 1460 loop : -0.31 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 90 HIS 0.008 0.002 HIS C 316 PHE 0.013 0.002 PHE D 143 TYR 0.015 0.002 TYR A 588 ARG 0.007 0.001 ARG B 909 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 216 time to evaluate : 4.128 Fit side-chains REVERT: A 92 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7889 (mmm) REVERT: A 103 VAL cc_start: 0.8874 (t) cc_final: 0.8654 (m) REVERT: A 170 GLU cc_start: 0.7237 (mt-10) cc_final: 0.7024 (mt-10) REVERT: A 661 LYS cc_start: 0.7966 (tttp) cc_final: 0.7754 (mttp) REVERT: A 910 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8469 (pp) REVERT: B 92 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7891 (mmm) REVERT: B 103 VAL cc_start: 0.8877 (t) cc_final: 0.8653 (m) REVERT: B 170 GLU cc_start: 0.7236 (mt-10) cc_final: 0.7023 (mt-10) REVERT: B 661 LYS cc_start: 0.7969 (tttp) cc_final: 0.7753 (mttp) REVERT: B 910 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8464 (pp) REVERT: C 92 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7888 (mmm) REVERT: C 103 VAL cc_start: 0.8875 (t) cc_final: 0.8653 (m) REVERT: C 170 GLU cc_start: 0.7232 (mt-10) cc_final: 0.7019 (mt-10) REVERT: C 661 LYS cc_start: 0.7970 (tttp) cc_final: 0.7756 (mttp) REVERT: C 910 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8466 (pp) REVERT: D 92 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7890 (mmm) REVERT: D 103 VAL cc_start: 0.8875 (t) cc_final: 0.8653 (m) REVERT: D 170 GLU cc_start: 0.7236 (mt-10) cc_final: 0.7025 (mt-10) REVERT: D 661 LYS cc_start: 0.7971 (tttp) cc_final: 0.7756 (mttp) REVERT: D 910 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8466 (pp) outliers start: 76 outliers final: 40 residues processed: 272 average time/residue: 0.4905 time to fit residues: 219.3481 Evaluate side-chains 256 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 208 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 0.0980 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 400 optimal weight: 0.9980 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 226 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS A1022 GLN B 135 GLN B 226 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 HIS C 135 GLN C 226 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS C1022 GLN D 135 GLN D 226 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS D1022 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33792 Z= 0.154 Angle : 0.453 8.852 46104 Z= 0.236 Chirality : 0.042 0.138 4820 Planarity : 0.003 0.037 6088 Dihedral : 4.339 39.462 4488 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 2.06 % Allowed : 15.30 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 4080 helix: 0.25 (0.23), residues: 524 sheet: 0.41 (0.13), residues: 1464 loop : -0.16 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 553 HIS 0.003 0.001 HIS A1015 PHE 0.006 0.001 PHE D 225 TYR 0.009 0.001 TYR A 906 ARG 0.002 0.000 ARG C 909 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 224 time to evaluate : 4.066 Fit side-chains REVERT: A 92 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7831 (mmm) REVERT: A 103 VAL cc_start: 0.8918 (t) cc_final: 0.8694 (m) REVERT: A 661 LYS cc_start: 0.8048 (tttp) cc_final: 0.7735 (mttp) REVERT: A 804 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8346 (m110) REVERT: A 910 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8445 (pp) REVERT: B 92 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7830 (mmm) REVERT: B 103 VAL cc_start: 0.8919 (t) cc_final: 0.8694 (m) REVERT: B 661 LYS cc_start: 0.8050 (tttp) cc_final: 0.7736 (mttp) REVERT: B 804 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8348 (m110) REVERT: B 910 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8440 (pp) REVERT: C 92 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7829 (mmm) REVERT: C 103 VAL cc_start: 0.8917 (t) cc_final: 0.8691 (m) REVERT: C 661 LYS cc_start: 0.8048 (tttp) cc_final: 0.7737 (mttp) REVERT: C 804 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8348 (m110) REVERT: C 910 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8444 (pp) REVERT: D 92 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7831 (mmm) REVERT: D 103 VAL cc_start: 0.8919 (t) cc_final: 0.8694 (m) REVERT: D 661 LYS cc_start: 0.8054 (tttp) cc_final: 0.7739 (mttp) REVERT: D 804 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8344 (m110) REVERT: D 910 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8443 (pp) outliers start: 72 outliers final: 28 residues processed: 280 average time/residue: 0.4996 time to fit residues: 221.9427 Evaluate side-chains 252 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 212 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 394 optimal weight: 7.9990 chunk 194 optimal weight: 0.0980 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN A 226 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 775 GLN ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 38 ASN B 135 GLN B 226 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 HIS B1022 GLN C 38 ASN C 135 GLN C 226 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 775 GLN ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS D 38 ASN D 135 GLN D 226 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 775 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33792 Z= 0.301 Angle : 0.517 9.338 46104 Z= 0.268 Chirality : 0.045 0.151 4820 Planarity : 0.004 0.036 6088 Dihedral : 4.611 45.212 4484 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 2.40 % Allowed : 14.42 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4080 helix: 0.30 (0.24), residues: 524 sheet: 0.42 (0.14), residues: 1460 loop : -0.20 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 90 HIS 0.006 0.001 HIS B1015 PHE 0.011 0.001 PHE C 143 TYR 0.014 0.002 TYR C 588 ARG 0.005 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 228 time to evaluate : 4.013 Fit side-chains REVERT: A 92 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7776 (mmm) REVERT: A 804 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8465 (t0) REVERT: A 906 TYR cc_start: 0.8709 (m-80) cc_final: 0.8119 (m-80) REVERT: A 910 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8506 (pp) REVERT: B 92 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7775 (mmm) REVERT: B 804 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8468 (t0) REVERT: B 906 TYR cc_start: 0.8705 (m-80) cc_final: 0.8115 (m-80) REVERT: B 910 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8503 (pp) REVERT: C 92 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7774 (mmm) REVERT: C 804 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8465 (t0) REVERT: C 906 TYR cc_start: 0.8710 (m-80) cc_final: 0.8116 (m-80) REVERT: C 910 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8503 (pp) REVERT: D 92 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7777 (mmm) REVERT: D 804 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8469 (t0) REVERT: D 906 TYR cc_start: 0.8711 (m-80) cc_final: 0.8117 (m-80) REVERT: D 910 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8503 (pp) outliers start: 84 outliers final: 44 residues processed: 296 average time/residue: 0.4642 time to fit residues: 225.5243 Evaluate side-chains 266 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 210 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN B 775 GLN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 718 GLN ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 33792 Z= 0.467 Angle : 0.616 9.566 46104 Z= 0.320 Chirality : 0.049 0.168 4820 Planarity : 0.005 0.041 6088 Dihedral : 5.086 45.100 4484 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 2.86 % Allowed : 13.96 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4080 helix: -0.04 (0.23), residues: 524 sheet: 0.24 (0.13), residues: 1460 loop : -0.34 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 90 HIS 0.009 0.002 HIS D1015 PHE 0.015 0.002 PHE D 143 TYR 0.020 0.003 TYR C 588 ARG 0.006 0.001 ARG C 909 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 212 time to evaluate : 4.293 Fit side-chains REVERT: A 92 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7820 (mmp) REVERT: A 214 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 804 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8451 (t0) REVERT: A 906 TYR cc_start: 0.8837 (m-80) cc_final: 0.8400 (m-80) REVERT: A 910 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8611 (pp) REVERT: B 92 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7826 (mmp) REVERT: B 214 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8267 (mp) REVERT: B 804 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8453 (t0) REVERT: B 906 TYR cc_start: 0.8830 (m-80) cc_final: 0.8396 (m-80) REVERT: B 910 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8608 (pp) REVERT: C 92 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7820 (mmp) REVERT: C 214 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8264 (mp) REVERT: C 804 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8451 (t0) REVERT: C 906 TYR cc_start: 0.8835 (m-80) cc_final: 0.8403 (m-80) REVERT: C 910 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8610 (pp) REVERT: D 92 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7820 (mmp) REVERT: D 214 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8265 (mp) REVERT: D 804 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8453 (t0) REVERT: D 906 TYR cc_start: 0.8833 (m-80) cc_final: 0.8399 (m-80) REVERT: D 910 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8608 (pp) outliers start: 100 outliers final: 52 residues processed: 292 average time/residue: 0.4620 time to fit residues: 221.9607 Evaluate side-chains 268 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 200 time to evaluate : 4.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 6.9990 chunk 355 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33792 Z= 0.300 Angle : 0.533 9.384 46104 Z= 0.278 Chirality : 0.045 0.157 4820 Planarity : 0.004 0.042 6088 Dihedral : 4.855 43.700 4484 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 2.26 % Allowed : 15.82 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4080 helix: 0.14 (0.24), residues: 524 sheet: 0.22 (0.13), residues: 1460 loop : -0.32 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 90 HIS 0.004 0.001 HIS D1015 PHE 0.008 0.001 PHE B 143 TYR 0.013 0.002 TYR C 123 ARG 0.004 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 200 time to evaluate : 3.884 Fit side-chains REVERT: A 92 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7803 (mmp) REVERT: A 486 TYR cc_start: 0.8804 (t80) cc_final: 0.8599 (t80) REVERT: A 804 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8482 (t0) REVERT: A 906 TYR cc_start: 0.8826 (m-80) cc_final: 0.8386 (m-80) REVERT: A 910 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8616 (pp) REVERT: B 92 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7806 (mmp) REVERT: B 804 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8483 (t0) REVERT: B 906 TYR cc_start: 0.8815 (m-80) cc_final: 0.8378 (m-80) REVERT: B 910 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8612 (pp) REVERT: C 92 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7804 (mmp) REVERT: C 804 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8484 (t0) REVERT: C 906 TYR cc_start: 0.8822 (m-80) cc_final: 0.8384 (m-80) REVERT: C 910 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8615 (pp) REVERT: D 92 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7801 (mmp) REVERT: D 486 TYR cc_start: 0.8804 (t80) cc_final: 0.8603 (t80) REVERT: D 804 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8484 (t0) REVERT: D 906 TYR cc_start: 0.8821 (m-80) cc_final: 0.8382 (m-80) REVERT: D 910 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8613 (pp) outliers start: 79 outliers final: 36 residues processed: 263 average time/residue: 0.4734 time to fit residues: 203.7716 Evaluate side-chains 250 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 202 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 33792 Z= 0.435 Angle : 0.597 9.567 46104 Z= 0.310 Chirality : 0.048 0.165 4820 Planarity : 0.005 0.047 6088 Dihedral : 5.100 45.803 4484 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 2.72 % Allowed : 15.05 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4080 helix: -0.06 (0.23), residues: 548 sheet: 0.08 (0.13), residues: 1460 loop : -0.44 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 90 HIS 0.007 0.001 HIS A1015 PHE 0.013 0.002 PHE A 143 TYR 0.018 0.002 TYR B 588 ARG 0.005 0.001 ARG B 909 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 194 time to evaluate : 4.082 Fit side-chains REVERT: A 40 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: A 92 MET cc_start: 0.8425 (mmm) cc_final: 0.7843 (mmp) REVERT: A 804 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8455 (t0) REVERT: A 906 TYR cc_start: 0.8835 (m-80) cc_final: 0.8402 (m-80) REVERT: A 910 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8668 (pp) REVERT: A 958 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8046 (p0) REVERT: A 984 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8785 (tp) REVERT: B 40 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: B 92 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7848 (mmp) REVERT: B 804 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8456 (t0) REVERT: B 906 TYR cc_start: 0.8828 (m-80) cc_final: 0.8399 (m-80) REVERT: B 910 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8666 (pp) REVERT: B 958 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8047 (p0) REVERT: B 984 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8789 (tp) REVERT: C 40 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: C 92 MET cc_start: 0.8428 (mmm) cc_final: 0.7847 (mmp) REVERT: C 804 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8455 (t0) REVERT: C 906 TYR cc_start: 0.8829 (m-80) cc_final: 0.8401 (m-80) REVERT: C 910 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8668 (pp) REVERT: C 958 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8046 (p0) REVERT: C 984 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8789 (tp) REVERT: D 40 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: D 92 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7845 (mmp) REVERT: D 804 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8455 (t0) REVERT: D 906 TYR cc_start: 0.8832 (m-80) cc_final: 0.8404 (m-80) REVERT: D 910 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8667 (pp) REVERT: D 958 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8048 (p0) REVERT: D 984 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8786 (tp) outliers start: 95 outliers final: 41 residues processed: 279 average time/residue: 0.4665 time to fit residues: 210.8342 Evaluate side-chains 251 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 188 time to evaluate : 3.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33792 Z= 0.178 Angle : 0.482 9.018 46104 Z= 0.252 Chirality : 0.043 0.158 4820 Planarity : 0.004 0.043 6088 Dihedral : 4.610 41.093 4484 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 1.52 % Allowed : 16.45 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4080 helix: 0.38 (0.23), residues: 548 sheet: 0.17 (0.13), residues: 1452 loop : -0.29 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 553 HIS 0.003 0.001 HIS C 653 PHE 0.007 0.001 PHE A 150 TYR 0.011 0.001 TYR A 906 ARG 0.002 0.000 ARG D 781 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 208 time to evaluate : 4.178 Fit side-chains REVERT: A 92 MET cc_start: 0.8460 (mmm) cc_final: 0.7928 (mmp) REVERT: A 423 MET cc_start: 0.8253 (mtt) cc_final: 0.7953 (ttm) REVERT: A 804 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8421 (t0) REVERT: A 906 TYR cc_start: 0.8817 (m-80) cc_final: 0.8347 (m-80) REVERT: A 910 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8630 (pp) REVERT: B 92 MET cc_start: 0.8464 (mmm) cc_final: 0.7931 (mmp) REVERT: B 423 MET cc_start: 0.8234 (mtt) cc_final: 0.7941 (ttm) REVERT: B 486 TYR cc_start: 0.8818 (t80) cc_final: 0.8599 (t80) REVERT: B 804 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8449 (t0) REVERT: B 906 TYR cc_start: 0.8812 (m-80) cc_final: 0.8345 (m-80) REVERT: B 910 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8627 (pp) REVERT: C 92 MET cc_start: 0.8460 (mmm) cc_final: 0.7931 (mmp) REVERT: C 423 MET cc_start: 0.8243 (mtt) cc_final: 0.7946 (ttm) REVERT: C 486 TYR cc_start: 0.8814 (t80) cc_final: 0.8593 (t80) REVERT: C 804 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8421 (t0) REVERT: C 906 TYR cc_start: 0.8817 (m-80) cc_final: 0.8347 (m-80) REVERT: C 910 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8630 (pp) REVERT: D 92 MET cc_start: 0.8462 (mmm) cc_final: 0.7927 (mmp) REVERT: D 423 MET cc_start: 0.8249 (mtt) cc_final: 0.7952 (ttm) REVERT: D 804 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8448 (t0) REVERT: D 906 TYR cc_start: 0.8816 (m-80) cc_final: 0.8350 (m-80) REVERT: D 910 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8628 (pp) outliers start: 53 outliers final: 32 residues processed: 249 average time/residue: 0.4813 time to fit residues: 193.5367 Evaluate side-chains 234 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.9990 chunk 376 optimal weight: 10.0000 chunk 343 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 331 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 365 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33792 Z= 0.201 Angle : 0.485 9.017 46104 Z= 0.252 Chirality : 0.043 0.156 4820 Planarity : 0.004 0.044 6088 Dihedral : 4.547 42.252 4484 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 1.46 % Allowed : 16.48 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 4080 helix: 0.50 (0.23), residues: 548 sheet: 0.16 (0.13), residues: 1460 loop : -0.27 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 553 HIS 0.003 0.001 HIS B 653 PHE 0.007 0.001 PHE D 150 TYR 0.011 0.001 TYR D 123 ARG 0.002 0.000 ARG C 909 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 4.559 Fit side-chains REVERT: A 92 MET cc_start: 0.8444 (mmm) cc_final: 0.7914 (mmp) REVERT: A 486 TYR cc_start: 0.8714 (t80) cc_final: 0.8459 (t80) REVERT: A 804 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8464 (t0) REVERT: A 906 TYR cc_start: 0.8726 (m-80) cc_final: 0.8237 (m-80) REVERT: A 910 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8598 (pp) REVERT: B 92 MET cc_start: 0.8449 (mmm) cc_final: 0.7941 (mmp) REVERT: B 804 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8468 (t0) REVERT: B 906 TYR cc_start: 0.8719 (m-80) cc_final: 0.8222 (m-80) REVERT: B 910 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8594 (pp) REVERT: B 958 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.7605 (p0) REVERT: C 92 MET cc_start: 0.8446 (mmm) cc_final: 0.7915 (mmp) REVERT: C 804 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8466 (t0) REVERT: C 906 TYR cc_start: 0.8724 (m-80) cc_final: 0.8224 (m-80) REVERT: C 910 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8597 (pp) REVERT: C 958 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7601 (p0) REVERT: D 92 MET cc_start: 0.8441 (mmm) cc_final: 0.7931 (mmp) REVERT: D 486 TYR cc_start: 0.8715 (t80) cc_final: 0.8461 (t80) REVERT: D 804 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8466 (t0) REVERT: D 906 TYR cc_start: 0.8725 (m-80) cc_final: 0.8239 (m-80) REVERT: D 910 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8596 (pp) outliers start: 51 outliers final: 34 residues processed: 245 average time/residue: 0.4783 time to fit residues: 188.8686 Evaluate side-chains 242 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 0.8980 chunk 374 optimal weight: 8.9990 chunk 323 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33792 Z= 0.190 Angle : 0.477 9.015 46104 Z= 0.248 Chirality : 0.043 0.156 4820 Planarity : 0.004 0.042 6088 Dihedral : 4.466 39.910 4484 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 1.34 % Allowed : 16.59 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4080 helix: 0.57 (0.24), residues: 548 sheet: 0.12 (0.13), residues: 1472 loop : -0.23 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 553 HIS 0.003 0.001 HIS B 464 PHE 0.007 0.001 PHE D 150 TYR 0.011 0.001 TYR D 123 ARG 0.002 0.000 ARG C 909 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 200 time to evaluate : 3.816 Fit side-chains REVERT: A 92 MET cc_start: 0.8440 (mmm) cc_final: 0.7938 (mmp) REVERT: A 486 TYR cc_start: 0.8784 (t80) cc_final: 0.8426 (t80) REVERT: A 804 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8467 (t0) REVERT: A 906 TYR cc_start: 0.8730 (m-80) cc_final: 0.8229 (m-80) REVERT: A 910 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8601 (pp) REVERT: A 958 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7588 (p0) REVERT: B 92 MET cc_start: 0.8455 (mmm) cc_final: 0.7941 (mmp) REVERT: B 486 TYR cc_start: 0.8742 (t80) cc_final: 0.8377 (t80) REVERT: B 804 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8470 (t0) REVERT: B 906 TYR cc_start: 0.8723 (m-80) cc_final: 0.8226 (m-80) REVERT: B 910 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8598 (pp) REVERT: B 958 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7541 (p0) REVERT: C 92 MET cc_start: 0.8443 (mmm) cc_final: 0.7941 (mmp) REVERT: C 486 TYR cc_start: 0.8737 (t80) cc_final: 0.8373 (t80) REVERT: C 804 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8469 (t0) REVERT: C 906 TYR cc_start: 0.8728 (m-80) cc_final: 0.8239 (m-80) REVERT: C 910 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8598 (pp) REVERT: D 92 MET cc_start: 0.8446 (mmm) cc_final: 0.7931 (mmp) REVERT: D 486 TYR cc_start: 0.8784 (t80) cc_final: 0.8428 (t80) REVERT: D 804 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8469 (t0) REVERT: D 906 TYR cc_start: 0.8729 (m-80) cc_final: 0.8229 (m-80) REVERT: D 910 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8598 (pp) REVERT: D 958 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7589 (p0) outliers start: 47 outliers final: 35 residues processed: 244 average time/residue: 0.4726 time to fit residues: 186.7026 Evaluate side-chains 242 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 324 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 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 = 0.3241 r_free = 0.3241 target = 0.099366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087480 restraints weight = 55435.774| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.60 r_work: 0.2979 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33792 Z= 0.198 Angle : 0.478 9.063 46104 Z= 0.248 Chirality : 0.043 0.155 4820 Planarity : 0.004 0.043 6088 Dihedral : 4.459 41.343 4484 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 1.40 % Allowed : 16.50 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 4080 helix: 0.59 (0.24), residues: 548 sheet: 0.26 (0.14), residues: 1432 loop : -0.31 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 553 HIS 0.003 0.001 HIS A 653 PHE 0.007 0.001 PHE D 150 TYR 0.011 0.001 TYR D 123 ARG 0.002 0.000 ARG D 909 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5827.68 seconds wall clock time: 107 minutes 58.94 seconds (6478.94 seconds total)