Starting phenix.real_space_refine on Mon Mar 18 11:20:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/03_2024/7f5u_31467.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/03_2024/7f5u_31467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/03_2024/7f5u_31467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/03_2024/7f5u_31467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/03_2024/7f5u_31467.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/03_2024/7f5u_31467.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 112 5.16 5 C 12992 2.51 5 N 3668 2.21 5 O 3972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 330": "NH1" <-> "NH2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ASP 448": "OD1" <-> "OD2" Residue "C GLU 451": "OE1" <-> "OE2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 551": "NH1" <-> "NH2" Residue "C TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ASP 207": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ASP 448": "OD1" <-> "OD2" Residue "D GLU 451": "OE1" <-> "OE2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20744 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5186 Classifications: {'peptide': 685} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 660} Chain breaks: 3 Chain: "B" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5186 Classifications: {'peptide': 685} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 660} Chain breaks: 3 Chain: "C" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5186 Classifications: {'peptide': 685} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 660} Chain breaks: 3 Chain: "D" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5186 Classifications: {'peptide': 685} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 660} Chain breaks: 3 Time building chain proxies: 10.59, per 1000 atoms: 0.51 Number of scatterers: 20744 At special positions: 0 Unit cell: (196.1, 96.46, 92.22, 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 112 16.00 O 3972 8.00 N 3668 7.00 C 12992 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: 8.87 Conformation dependent library (CDL) restraints added in 3.7 seconds 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 36 sheets defined 49.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.612A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 94 Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.678A pdb=" N PHE A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.717A pdb=" N ASN A 128 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 163 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.630A pdb=" N LEU A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.902A pdb=" N ALA A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.522A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 471 through 484 removed outlier: 4.223A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 removed outlier: 4.199A pdb=" N VAL A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.508A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.549A pdb=" N ALA A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.966A pdb=" N SER A 612 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 Processing helix chain 'A' and resid 633 through 640 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.506A pdb=" N ALA A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.604A pdb=" N ALA A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.612A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 94 Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.678A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.717A pdb=" N ASN B 128 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 163 Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 232 through 245 removed outlier: 3.630A pdb=" N LEU B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 348 through 364 removed outlier: 3.902A pdb=" N ALA B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 403 removed outlier: 3.522A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 433 Processing helix chain 'B' and resid 471 through 484 removed outlier: 4.223A pdb=" N GLN B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 removed outlier: 4.199A pdb=" N VAL B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.508A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 removed outlier: 3.549A pdb=" N ALA B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.966A pdb=" N SER B 612 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 633 through 640 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 removed outlier: 3.506A pdb=" N ALA B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.604A pdb=" N ALA B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.612A pdb=" N ILE C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 94 Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.678A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.717A pdb=" N ASN C 128 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 163 Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 180 through 197 Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.630A pdb=" N LEU C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 348 through 364 removed outlier: 3.902A pdb=" N ALA C 352 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.522A pdb=" N LYS C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 415 through 433 Processing helix chain 'C' and resid 471 through 484 removed outlier: 4.223A pdb=" N GLN C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 513 removed outlier: 4.199A pdb=" N VAL C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.508A pdb=" N LEU C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 557 Processing helix chain 'C' and resid 579 through 592 removed outlier: 3.549A pdb=" N ALA C 583 " --> pdb=" O ASP C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.966A pdb=" N SER C 612 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 Processing helix chain 'C' and resid 633 through 640 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 689 through 700 removed outlier: 3.506A pdb=" N ALA C 693 " --> pdb=" O ASN C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 714 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 756 through 761 removed outlier: 3.604A pdb=" N ALA C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 64 through 69 removed outlier: 3.612A pdb=" N ILE D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 94 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.678A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.717A pdb=" N ASN D 128 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 163 Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 180 through 197 Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.630A pdb=" N LEU D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 348 through 364 removed outlier: 3.902A pdb=" N ALA D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA D 364 " --> pdb=" O ARG D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 384 Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.522A pdb=" N LYS D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 Processing helix chain 'D' and resid 415 through 433 Processing helix chain 'D' and resid 471 through 484 removed outlier: 4.223A pdb=" N GLN D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 513 removed outlier: 4.199A pdb=" N VAL D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 534 removed outlier: 3.508A pdb=" N LEU D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 579 through 592 removed outlier: 3.549A pdb=" N ALA D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.966A pdb=" N SER D 612 " --> pdb=" O ASP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 626 Processing helix chain 'D' and resid 633 through 640 Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 689 through 700 removed outlier: 3.506A pdb=" N ALA D 693 " --> pdb=" O ASN D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 714 Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 756 through 761 removed outlier: 3.604A pdb=" N ALA D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 6.490A pdb=" N LEU A 249 " --> pdb=" O VAL A 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 751 removed outlier: 3.515A pdb=" N GLU A 751 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 451 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 444 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 520 through 521 removed outlier: 5.949A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS A 490 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 464 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 662 through 664 removed outlier: 5.556A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 572 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS A 607 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 574 " --> pdb=" O HIS A 607 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR A 573 " --> pdb=" O VAL A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 630 removed outlier: 7.014A pdb=" N LYS A 629 " --> pdb=" O CYS A 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 726 through 728 removed outlier: 4.128A pdb=" N GLY A 726 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 738 " --> pdb=" O GLY A 726 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AB2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AB3, first strand: chain 'B' and resid 248 through 250 removed outlier: 6.490A pdb=" N LEU B 249 " --> pdb=" O VAL B 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AB5, first strand: chain 'B' and resid 744 through 751 removed outlier: 3.515A pdb=" N GLU B 751 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B 451 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 444 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 520 through 521 removed outlier: 5.949A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS B 490 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 464 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 662 through 664 removed outlier: 5.556A pdb=" N ILE B 606 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL B 572 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS B 607 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 574 " --> pdb=" O HIS B 607 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR B 573 " --> pdb=" O VAL B 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 629 through 630 removed outlier: 7.014A pdb=" N LYS B 629 " --> pdb=" O CYS B 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 726 through 728 removed outlier: 4.128A pdb=" N GLY B 726 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 738 " --> pdb=" O GLY B 726 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'C' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'C' and resid 248 through 250 removed outlier: 6.490A pdb=" N LEU C 249 " --> pdb=" O VAL C 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 273 through 274 Processing sheet with id=AC5, first strand: chain 'C' and resid 744 through 751 removed outlier: 3.515A pdb=" N GLU C 751 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU C 451 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C 444 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 520 through 521 removed outlier: 5.949A pdb=" N LEU C 462 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS C 490 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL C 464 " --> pdb=" O LYS C 490 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 662 through 664 removed outlier: 5.556A pdb=" N ILE C 606 " --> pdb=" O VAL C 664 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL C 572 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS C 607 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE C 574 " --> pdb=" O HIS C 607 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR C 573 " --> pdb=" O VAL C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 629 through 630 removed outlier: 7.014A pdb=" N LYS C 629 " --> pdb=" O CYS C 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 726 through 728 removed outlier: 4.128A pdb=" N GLY C 726 " --> pdb=" O VAL C 738 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 738 " --> pdb=" O GLY C 726 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 58 through 59 Processing sheet with id=AD2, first strand: chain 'D' and resid 171 through 173 Processing sheet with id=AD3, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.490A pdb=" N LEU D 249 " --> pdb=" O VAL D 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AD5, first strand: chain 'D' and resid 744 through 751 removed outlier: 3.515A pdb=" N GLU D 751 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 451 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 444 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 520 through 521 removed outlier: 5.949A pdb=" N LEU D 462 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS D 490 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL D 464 " --> pdb=" O LYS D 490 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 662 through 664 removed outlier: 5.556A pdb=" N ILE D 606 " --> pdb=" O VAL D 664 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL D 572 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS D 607 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE D 574 " --> pdb=" O HIS D 607 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR D 573 " --> pdb=" O VAL D 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 629 through 630 removed outlier: 7.014A pdb=" N LYS D 629 " --> pdb=" O CYS D 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 726 through 728 removed outlier: 4.128A pdb=" N GLY D 726 " --> pdb=" O VAL D 738 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 738 " --> pdb=" O GLY D 726 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2712 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: 7.10 Time building geometry restraints manager: 9.49 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: 7100 1.34 - 1.46: 3804 1.46 - 1.57: 9960 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 21048 Sorted by residual: bond pdb=" CA SER B 679 " pdb=" C SER B 679 " ideal model delta sigma weight residual 1.524 1.489 0.036 1.66e-02 3.63e+03 4.64e+00 bond pdb=" CA SER A 679 " pdb=" C SER A 679 " ideal model delta sigma weight residual 1.524 1.489 0.036 1.66e-02 3.63e+03 4.64e+00 bond pdb=" CA SER D 679 " pdb=" C SER D 679 " ideal model delta sigma weight residual 1.524 1.489 0.036 1.66e-02 3.63e+03 4.64e+00 bond pdb=" CA SER C 679 " pdb=" C SER C 679 " ideal model delta sigma weight residual 1.524 1.489 0.036 1.66e-02 3.63e+03 4.64e+00 bond pdb=" C VAL A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 1.334 1.295 0.039 2.34e-02 1.83e+03 2.83e+00 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.65: 400 105.65 - 112.73: 11980 112.73 - 119.80: 6288 119.80 - 126.87: 9620 126.87 - 133.94: 196 Bond angle restraints: 28484 Sorted by residual: angle pdb=" N VAL B 209 " pdb=" CA VAL B 209 " pdb=" C VAL B 209 " ideal model delta sigma weight residual 113.53 108.48 5.05 9.80e-01 1.04e+00 2.66e+01 angle pdb=" N VAL D 209 " pdb=" CA VAL D 209 " pdb=" C VAL D 209 " ideal model delta sigma weight residual 113.53 108.48 5.05 9.80e-01 1.04e+00 2.66e+01 angle pdb=" N VAL A 209 " pdb=" CA VAL A 209 " pdb=" C VAL A 209 " ideal model delta sigma weight residual 113.53 108.48 5.05 9.80e-01 1.04e+00 2.66e+01 angle pdb=" N VAL C 209 " pdb=" CA VAL C 209 " pdb=" C VAL C 209 " ideal model delta sigma weight residual 113.53 108.48 5.05 9.80e-01 1.04e+00 2.66e+01 angle pdb=" C VAL C 209 " pdb=" N SER C 210 " pdb=" CA SER C 210 " ideal model delta sigma weight residual 122.74 118.98 3.76 1.06e+00 8.90e-01 1.26e+01 ... (remaining 28479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 11540 17.68 - 35.35: 1060 35.35 - 53.03: 240 53.03 - 70.71: 32 70.71 - 88.38: 20 Dihedral angle restraints: 12892 sinusoidal: 5020 harmonic: 7872 Sorted by residual: dihedral pdb=" CA VAL B 348 " pdb=" C VAL B 348 " pdb=" N GLU B 349 " pdb=" CA GLU B 349 " ideal model delta harmonic sigma weight residual -180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA VAL D 348 " pdb=" C VAL D 348 " pdb=" N GLU D 349 " pdb=" CA GLU D 349 " ideal model delta harmonic sigma weight residual 180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA VAL C 348 " pdb=" C VAL C 348 " pdb=" N GLU C 349 " pdb=" CA GLU C 349 " ideal model delta harmonic sigma weight residual 180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 12889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1852 0.029 - 0.058: 988 0.058 - 0.086: 304 0.086 - 0.115: 184 0.115 - 0.144: 32 Chirality restraints: 3360 Sorted by residual: chirality pdb=" CA VAL B 313 " pdb=" N VAL B 313 " pdb=" C VAL B 313 " pdb=" CB VAL B 313 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA VAL D 313 " pdb=" N VAL D 313 " pdb=" C VAL D 313 " pdb=" CB VAL D 313 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA VAL C 313 " pdb=" N VAL C 313 " pdb=" C VAL C 313 " pdb=" CB VAL C 313 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 3357 not shown) Planarity restraints: 3696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 524 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR C 524 " -0.029 2.00e-02 2.50e+03 pdb=" O THR C 524 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG C 525 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 524 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR A 524 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A 524 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 525 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 524 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR D 524 " 0.029 2.00e-02 2.50e+03 pdb=" O THR D 524 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG D 525 " -0.009 2.00e-02 2.50e+03 ... (remaining 3693 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 780 2.66 - 3.22: 23964 3.22 - 3.78: 33516 3.78 - 4.34: 44046 4.34 - 4.90: 68032 Nonbonded interactions: 170338 Sorted by model distance: nonbonded pdb=" O ALA C 509 " pdb=" OG1 THR C 512 " model vdw 2.101 2.440 nonbonded pdb=" O ALA A 509 " pdb=" OG1 THR A 512 " model vdw 2.101 2.440 nonbonded pdb=" O ALA B 509 " pdb=" OG1 THR B 512 " model vdw 2.101 2.440 nonbonded pdb=" O ALA D 509 " pdb=" OG1 THR D 512 " model vdw 2.101 2.440 nonbonded pdb=" O ASN D 672 " pdb=" OG1 THR D 676 " model vdw 2.159 2.440 ... (remaining 170333 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.010 Extract box with map and model: 6.590 Check model and map are aligned: 0.300 Set scattering table: 0.160 Process input model: 55.670 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.100 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.007 0.048 21048 Z= 0.445 Angle : 0.797 9.314 28484 Z= 0.461 Chirality : 0.043 0.144 3360 Planarity : 0.004 0.039 3696 Dihedral : 14.712 88.382 7788 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.26 % Favored : 87.59 % Rotamer: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.14), residues: 2708 helix: -2.22 (0.13), residues: 1196 sheet: -4.34 (0.17), residues: 452 loop : -3.19 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 768 HIS 0.008 0.001 HIS D 517 PHE 0.012 0.002 PHE B 760 TYR 0.013 0.002 TYR D 55 ARG 0.004 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 271 MET cc_start: 0.7778 (tpp) cc_final: 0.6644 (mmt) REVERT: A 318 MET cc_start: 0.7948 (mpp) cc_final: 0.7612 (mpp) REVERT: A 605 LEU cc_start: 0.9445 (tp) cc_final: 0.9074 (mp) REVERT: A 677 TYR cc_start: 0.9325 (m-80) cc_final: 0.9075 (m-80) REVERT: B 193 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8583 (tm-30) REVERT: B 271 MET cc_start: 0.7789 (tpp) cc_final: 0.6655 (mmt) REVERT: B 318 MET cc_start: 0.7948 (mpp) cc_final: 0.7606 (mpp) REVERT: B 605 LEU cc_start: 0.9456 (tp) cc_final: 0.9089 (mp) REVERT: B 677 TYR cc_start: 0.9335 (m-80) cc_final: 0.9080 (m-80) REVERT: C 193 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8596 (tm-30) REVERT: C 271 MET cc_start: 0.7778 (tpp) cc_final: 0.6651 (mmt) REVERT: C 318 MET cc_start: 0.7944 (mpp) cc_final: 0.7615 (mpp) REVERT: C 605 LEU cc_start: 0.9438 (tp) cc_final: 0.9060 (mp) REVERT: C 677 TYR cc_start: 0.9314 (m-80) cc_final: 0.9074 (m-80) REVERT: D 193 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8586 (tm-30) REVERT: D 271 MET cc_start: 0.7781 (tpp) cc_final: 0.6650 (mmt) REVERT: D 318 MET cc_start: 0.7944 (mpp) cc_final: 0.7612 (mpp) REVERT: D 605 LEU cc_start: 0.9439 (tp) cc_final: 0.9063 (mp) REVERT: D 677 TYR cc_start: 0.9308 (m-80) cc_final: 0.9065 (m-80) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.3943 time to fit residues: 147.9394 Evaluate side-chains 196 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 213 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 247 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 186 ASN A 369 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS B 92 HIS B 186 ASN B 369 GLN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS C 92 HIS C 186 ASN C 369 GLN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 HIS D 92 HIS D 186 ASN D 369 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21048 Z= 0.161 Angle : 0.601 8.288 28484 Z= 0.302 Chirality : 0.042 0.143 3360 Planarity : 0.004 0.036 3696 Dihedral : 4.823 25.391 2912 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.83 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.16), residues: 2708 helix: -0.43 (0.14), residues: 1276 sheet: -3.89 (0.18), residues: 464 loop : -2.73 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 748 HIS 0.002 0.001 HIS C 733 PHE 0.015 0.001 PHE B 760 TYR 0.010 0.001 TYR A 157 ARG 0.004 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 207 ASP cc_start: 0.8830 (p0) cc_final: 0.8586 (p0) REVERT: A 271 MET cc_start: 0.6776 (tpp) cc_final: 0.6256 (tpp) REVERT: A 318 MET cc_start: 0.7928 (mpp) cc_final: 0.7706 (mpp) REVERT: A 570 CYS cc_start: 0.8772 (m) cc_final: 0.8248 (m) REVERT: A 601 MET cc_start: 0.8104 (tmm) cc_final: 0.7634 (tmm) REVERT: A 605 LEU cc_start: 0.9429 (tp) cc_final: 0.9116 (mp) REVERT: B 90 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 207 ASP cc_start: 0.8820 (p0) cc_final: 0.8577 (p0) REVERT: B 271 MET cc_start: 0.6790 (tpp) cc_final: 0.6259 (tpp) REVERT: B 318 MET cc_start: 0.7926 (mpp) cc_final: 0.7703 (mpp) REVERT: B 570 CYS cc_start: 0.8774 (m) cc_final: 0.8255 (m) REVERT: B 601 MET cc_start: 0.8105 (tmm) cc_final: 0.7636 (tmm) REVERT: B 605 LEU cc_start: 0.9438 (tp) cc_final: 0.9129 (mp) REVERT: C 90 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7772 (mm-30) REVERT: C 207 ASP cc_start: 0.8840 (p0) cc_final: 0.8588 (p0) REVERT: C 271 MET cc_start: 0.6782 (tpp) cc_final: 0.6253 (tpp) REVERT: C 318 MET cc_start: 0.7925 (mpp) cc_final: 0.7710 (mpp) REVERT: C 570 CYS cc_start: 0.8759 (m) cc_final: 0.8242 (m) REVERT: C 601 MET cc_start: 0.8100 (tmm) cc_final: 0.7632 (tmm) REVERT: C 605 LEU cc_start: 0.9422 (tp) cc_final: 0.9102 (mp) REVERT: D 90 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7775 (mm-30) REVERT: D 207 ASP cc_start: 0.8820 (p0) cc_final: 0.8573 (p0) REVERT: D 271 MET cc_start: 0.6789 (tpp) cc_final: 0.6255 (tpp) REVERT: D 318 MET cc_start: 0.7919 (mpp) cc_final: 0.7701 (mpp) REVERT: D 570 CYS cc_start: 0.8757 (m) cc_final: 0.8243 (m) REVERT: D 601 MET cc_start: 0.8120 (tmm) cc_final: 0.7652 (tmm) REVERT: D 605 LEU cc_start: 0.9424 (tp) cc_final: 0.9107 (mp) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.3524 time to fit residues: 162.7380 Evaluate side-chains 212 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN A 392 ASN A 454 GLN A 565 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 454 GLN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN C 392 ASN C 454 GLN C 565 HIS ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN D 454 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21048 Z= 0.320 Angle : 0.662 7.214 28484 Z= 0.338 Chirality : 0.043 0.146 3360 Planarity : 0.005 0.043 3696 Dihedral : 5.097 26.521 2912 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.78 % Favored : 89.07 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.16), residues: 2708 helix: -0.09 (0.14), residues: 1284 sheet: -3.65 (0.20), residues: 456 loop : -2.45 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 304 HIS 0.006 0.001 HIS D 517 PHE 0.024 0.002 PHE D 696 TYR 0.008 0.001 TYR B 157 ARG 0.006 0.000 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7797 (mm-30) REVERT: A 118 LEU cc_start: 0.9109 (mm) cc_final: 0.8759 (tp) REVERT: A 207 ASP cc_start: 0.8842 (p0) cc_final: 0.8610 (p0) REVERT: A 318 MET cc_start: 0.7955 (mpp) cc_final: 0.7533 (mpp) REVERT: A 487 LEU cc_start: 0.9406 (tt) cc_final: 0.9171 (tp) REVERT: A 570 CYS cc_start: 0.8817 (m) cc_final: 0.8325 (m) REVERT: A 601 MET cc_start: 0.8143 (tmm) cc_final: 0.7715 (tmm) REVERT: A 605 LEU cc_start: 0.9459 (tp) cc_final: 0.9153 (tp) REVERT: B 90 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 118 LEU cc_start: 0.9109 (mm) cc_final: 0.8757 (tp) REVERT: B 207 ASP cc_start: 0.8838 (p0) cc_final: 0.8602 (p0) REVERT: B 318 MET cc_start: 0.7950 (mpp) cc_final: 0.7522 (mpp) REVERT: B 487 LEU cc_start: 0.9406 (tt) cc_final: 0.9171 (tp) REVERT: B 570 CYS cc_start: 0.8814 (m) cc_final: 0.8327 (m) REVERT: B 601 MET cc_start: 0.8139 (tmm) cc_final: 0.7715 (tmm) REVERT: B 605 LEU cc_start: 0.9469 (tp) cc_final: 0.9164 (tp) REVERT: C 90 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 118 LEU cc_start: 0.9114 (mm) cc_final: 0.8765 (tp) REVERT: C 207 ASP cc_start: 0.8853 (p0) cc_final: 0.8613 (p0) REVERT: C 318 MET cc_start: 0.7950 (mpp) cc_final: 0.7530 (mpp) REVERT: C 487 LEU cc_start: 0.9408 (tt) cc_final: 0.9174 (tp) REVERT: C 570 CYS cc_start: 0.8809 (m) cc_final: 0.8323 (m) REVERT: C 601 MET cc_start: 0.8136 (tmm) cc_final: 0.7711 (tmm) REVERT: C 605 LEU cc_start: 0.9454 (tp) cc_final: 0.9147 (tp) REVERT: D 90 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7804 (mm-30) REVERT: D 118 LEU cc_start: 0.9110 (mm) cc_final: 0.8760 (tp) REVERT: D 207 ASP cc_start: 0.8835 (p0) cc_final: 0.8599 (p0) REVERT: D 318 MET cc_start: 0.7946 (mpp) cc_final: 0.7527 (mpp) REVERT: D 487 LEU cc_start: 0.9408 (tt) cc_final: 0.9171 (tp) REVERT: D 570 CYS cc_start: 0.8802 (m) cc_final: 0.8323 (m) REVERT: D 601 MET cc_start: 0.8157 (tmm) cc_final: 0.7733 (tmm) REVERT: D 605 LEU cc_start: 0.9454 (tp) cc_final: 0.9147 (tp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3223 time to fit residues: 113.4945 Evaluate side-chains 185 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 235 optimal weight: 0.0870 chunk 70 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 565 HIS ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21048 Z= 0.291 Angle : 0.648 7.949 28484 Z= 0.328 Chirality : 0.042 0.156 3360 Planarity : 0.004 0.042 3696 Dihedral : 5.027 25.607 2912 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2708 helix: 0.22 (0.15), residues: 1288 sheet: -3.47 (0.20), residues: 456 loop : -2.42 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 304 HIS 0.004 0.001 HIS B 673 PHE 0.017 0.001 PHE B 696 TYR 0.006 0.001 TYR D 55 ARG 0.006 0.001 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 118 LEU cc_start: 0.9084 (mm) cc_final: 0.8739 (tp) REVERT: A 119 MET cc_start: 0.8184 (tmm) cc_final: 0.7879 (tmm) REVERT: A 207 ASP cc_start: 0.8843 (p0) cc_final: 0.8598 (p0) REVERT: A 271 MET cc_start: 0.7478 (tpp) cc_final: 0.7202 (tpp) REVERT: A 318 MET cc_start: 0.7944 (mpp) cc_final: 0.7493 (mpp) REVERT: A 570 CYS cc_start: 0.8883 (m) cc_final: 0.8365 (m) REVERT: A 601 MET cc_start: 0.8132 (tmm) cc_final: 0.7698 (tmm) REVERT: A 677 TYR cc_start: 0.9216 (m-80) cc_final: 0.8961 (m-80) REVERT: B 90 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7851 (mm-30) REVERT: B 118 LEU cc_start: 0.9084 (mm) cc_final: 0.8735 (tp) REVERT: B 119 MET cc_start: 0.8188 (tmm) cc_final: 0.7885 (tmm) REVERT: B 207 ASP cc_start: 0.8839 (p0) cc_final: 0.8591 (p0) REVERT: B 271 MET cc_start: 0.7485 (tpp) cc_final: 0.7214 (tpp) REVERT: B 318 MET cc_start: 0.7940 (mpp) cc_final: 0.7484 (mpp) REVERT: B 570 CYS cc_start: 0.8887 (m) cc_final: 0.8372 (m) REVERT: B 601 MET cc_start: 0.8129 (tmm) cc_final: 0.7698 (tmm) REVERT: B 677 TYR cc_start: 0.9229 (m-80) cc_final: 0.8968 (m-80) REVERT: C 90 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 118 LEU cc_start: 0.9088 (mm) cc_final: 0.8743 (tp) REVERT: C 119 MET cc_start: 0.8181 (tmm) cc_final: 0.7874 (tmm) REVERT: C 207 ASP cc_start: 0.8853 (p0) cc_final: 0.8602 (p0) REVERT: C 271 MET cc_start: 0.7475 (tpp) cc_final: 0.7211 (tpp) REVERT: C 318 MET cc_start: 0.7939 (mpp) cc_final: 0.7490 (mpp) REVERT: C 570 CYS cc_start: 0.8872 (m) cc_final: 0.8361 (m) REVERT: C 601 MET cc_start: 0.8122 (tmm) cc_final: 0.7692 (tmm) REVERT: C 677 TYR cc_start: 0.9207 (m-80) cc_final: 0.8957 (m-80) REVERT: D 90 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7841 (mm-30) REVERT: D 118 LEU cc_start: 0.9083 (mm) cc_final: 0.8737 (tp) REVERT: D 119 MET cc_start: 0.8177 (tmm) cc_final: 0.7872 (tmm) REVERT: D 207 ASP cc_start: 0.8834 (p0) cc_final: 0.8586 (p0) REVERT: D 271 MET cc_start: 0.7484 (tpp) cc_final: 0.7210 (tpp) REVERT: D 318 MET cc_start: 0.7934 (mpp) cc_final: 0.7489 (mpp) REVERT: D 570 CYS cc_start: 0.8872 (m) cc_final: 0.8362 (m) REVERT: D 601 MET cc_start: 0.8143 (tmm) cc_final: 0.7711 (tmm) REVERT: D 677 TYR cc_start: 0.9197 (m-80) cc_final: 0.8948 (m-80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3138 time to fit residues: 108.1473 Evaluate side-chains 176 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 108 optimal weight: 0.0060 chunk 224 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 369 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 369 GLN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 369 GLN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 369 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21048 Z= 0.201 Angle : 0.596 6.600 28484 Z= 0.301 Chirality : 0.041 0.143 3360 Planarity : 0.004 0.040 3696 Dihedral : 4.736 25.488 2912 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.71 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.17), residues: 2708 helix: 0.46 (0.15), residues: 1300 sheet: -3.15 (0.21), residues: 464 loop : -2.30 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 304 HIS 0.002 0.001 HIS C 733 PHE 0.012 0.001 PHE B 696 TYR 0.010 0.001 TYR B 157 ARG 0.004 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 118 LEU cc_start: 0.8948 (mm) cc_final: 0.8735 (tp) REVERT: A 207 ASP cc_start: 0.8811 (p0) cc_final: 0.8547 (p0) REVERT: A 318 MET cc_start: 0.7950 (mpp) cc_final: 0.7522 (mpp) REVERT: A 570 CYS cc_start: 0.8821 (m) cc_final: 0.8327 (m) REVERT: A 601 MET cc_start: 0.8203 (tmm) cc_final: 0.7783 (tmm) REVERT: A 677 TYR cc_start: 0.9103 (m-80) cc_final: 0.8776 (m-80) REVERT: B 90 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7833 (mm-30) REVERT: B 118 LEU cc_start: 0.8949 (mm) cc_final: 0.8732 (tp) REVERT: B 207 ASP cc_start: 0.8803 (p0) cc_final: 0.8538 (p0) REVERT: B 318 MET cc_start: 0.7946 (mpp) cc_final: 0.7517 (mpp) REVERT: B 570 CYS cc_start: 0.8827 (m) cc_final: 0.8339 (m) REVERT: B 601 MET cc_start: 0.8199 (tmm) cc_final: 0.7783 (tmm) REVERT: B 677 TYR cc_start: 0.9118 (m-80) cc_final: 0.8783 (m-80) REVERT: C 90 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7825 (mm-30) REVERT: C 118 LEU cc_start: 0.8953 (mm) cc_final: 0.8740 (tp) REVERT: C 207 ASP cc_start: 0.8821 (p0) cc_final: 0.8551 (p0) REVERT: C 318 MET cc_start: 0.7949 (mpp) cc_final: 0.7526 (mpp) REVERT: C 570 CYS cc_start: 0.8813 (m) cc_final: 0.8326 (m) REVERT: C 601 MET cc_start: 0.8191 (tmm) cc_final: 0.7774 (tmm) REVERT: C 677 TYR cc_start: 0.9093 (m-80) cc_final: 0.8775 (m-80) REVERT: D 90 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7824 (mm-30) REVERT: D 118 LEU cc_start: 0.8947 (mm) cc_final: 0.8733 (tp) REVERT: D 207 ASP cc_start: 0.8800 (p0) cc_final: 0.8534 (p0) REVERT: D 318 MET cc_start: 0.7947 (mpp) cc_final: 0.7521 (mpp) REVERT: D 570 CYS cc_start: 0.8816 (m) cc_final: 0.8333 (m) REVERT: D 601 MET cc_start: 0.8213 (tmm) cc_final: 0.7795 (tmm) REVERT: D 677 TYR cc_start: 0.9082 (m-80) cc_final: 0.8762 (m-80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2887 time to fit residues: 101.5450 Evaluate side-chains 180 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 51 optimal weight: 0.0670 chunk 154 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 263 optimal weight: 0.9980 chunk 218 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 87 optimal weight: 0.2980 chunk 138 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 599 ASN B 375 ASN B 599 ASN C 375 ASN C 599 ASN D 375 ASN D 599 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21048 Z= 0.138 Angle : 0.557 5.868 28484 Z= 0.278 Chirality : 0.041 0.157 3360 Planarity : 0.004 0.038 3696 Dihedral : 4.327 24.004 2912 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.50 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2708 helix: 0.81 (0.15), residues: 1304 sheet: -2.77 (0.21), residues: 464 loop : -2.07 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 304 HIS 0.002 0.001 HIS C 537 PHE 0.007 0.001 PHE D 696 TYR 0.010 0.001 TYR C 157 ARG 0.004 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8943 (mm) cc_final: 0.8696 (tp) REVERT: A 123 MET cc_start: 0.8216 (ttm) cc_final: 0.7972 (ttm) REVERT: A 207 ASP cc_start: 0.8758 (p0) cc_final: 0.8495 (p0) REVERT: A 318 MET cc_start: 0.7989 (mpp) cc_final: 0.7579 (mpp) REVERT: A 601 MET cc_start: 0.8151 (tmm) cc_final: 0.7870 (tmm) REVERT: A 677 TYR cc_start: 0.9079 (m-80) cc_final: 0.8757 (m-80) REVERT: B 118 LEU cc_start: 0.8946 (mm) cc_final: 0.8696 (tp) REVERT: B 123 MET cc_start: 0.8235 (ttm) cc_final: 0.7995 (ttm) REVERT: B 207 ASP cc_start: 0.8753 (p0) cc_final: 0.8492 (p0) REVERT: B 318 MET cc_start: 0.7985 (mpp) cc_final: 0.7563 (mpp) REVERT: B 601 MET cc_start: 0.8152 (tmm) cc_final: 0.7870 (tmm) REVERT: B 677 TYR cc_start: 0.9095 (m-80) cc_final: 0.8766 (m-80) REVERT: C 118 LEU cc_start: 0.8946 (mm) cc_final: 0.8700 (tp) REVERT: C 123 MET cc_start: 0.8222 (ttm) cc_final: 0.7981 (ttm) REVERT: C 207 ASP cc_start: 0.8769 (p0) cc_final: 0.8501 (p0) REVERT: C 318 MET cc_start: 0.7986 (mpp) cc_final: 0.7578 (mpp) REVERT: C 601 MET cc_start: 0.8140 (tmm) cc_final: 0.7865 (tmm) REVERT: C 677 TYR cc_start: 0.9066 (m-80) cc_final: 0.8755 (m-80) REVERT: D 118 LEU cc_start: 0.8942 (mm) cc_final: 0.8695 (tp) REVERT: D 123 MET cc_start: 0.8228 (ttm) cc_final: 0.7991 (ttm) REVERT: D 207 ASP cc_start: 0.8750 (p0) cc_final: 0.8487 (p0) REVERT: D 318 MET cc_start: 0.7984 (mpp) cc_final: 0.7574 (mpp) REVERT: D 601 MET cc_start: 0.8166 (tmm) cc_final: 0.7884 (tmm) REVERT: D 677 TYR cc_start: 0.9055 (m-80) cc_final: 0.8746 (m-80) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3251 time to fit residues: 127.1972 Evaluate side-chains 192 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN B 344 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN C 344 ASN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN D 344 ASN ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 21048 Z= 0.309 Angle : 0.643 9.170 28484 Z= 0.324 Chirality : 0.041 0.145 3360 Planarity : 0.004 0.040 3696 Dihedral : 4.841 25.550 2912 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.68 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2708 helix: 0.87 (0.15), residues: 1300 sheet: -2.78 (0.22), residues: 464 loop : -2.01 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 304 HIS 0.004 0.001 HIS B 517 PHE 0.007 0.001 PHE D 178 TYR 0.009 0.001 TYR A 164 ARG 0.003 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9066 (mm) cc_final: 0.8811 (tp) REVERT: A 125 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8790 (tp30) REVERT: A 207 ASP cc_start: 0.8821 (p0) cc_final: 0.8567 (p0) REVERT: A 318 MET cc_start: 0.7982 (mpp) cc_final: 0.7495 (mpp) REVERT: A 534 MET cc_start: 0.8974 (tmm) cc_final: 0.8674 (tmm) REVERT: A 570 CYS cc_start: 0.8885 (m) cc_final: 0.8415 (m) REVERT: A 601 MET cc_start: 0.8177 (tmm) cc_final: 0.7908 (tmm) REVERT: A 677 TYR cc_start: 0.9213 (m-80) cc_final: 0.8832 (m-80) REVERT: B 118 LEU cc_start: 0.9068 (mm) cc_final: 0.8809 (tp) REVERT: B 125 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8789 (tp30) REVERT: B 207 ASP cc_start: 0.8815 (p0) cc_final: 0.8560 (p0) REVERT: B 318 MET cc_start: 0.7975 (mpp) cc_final: 0.7486 (mpp) REVERT: B 534 MET cc_start: 0.8969 (tmm) cc_final: 0.8669 (tmm) REVERT: B 570 CYS cc_start: 0.8864 (m) cc_final: 0.8402 (m) REVERT: B 601 MET cc_start: 0.8177 (tmm) cc_final: 0.7907 (tmm) REVERT: B 677 TYR cc_start: 0.9225 (m-80) cc_final: 0.8838 (m-80) REVERT: C 118 LEU cc_start: 0.9070 (mm) cc_final: 0.8816 (tp) REVERT: C 125 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8790 (tp30) REVERT: C 207 ASP cc_start: 0.8830 (p0) cc_final: 0.8574 (p0) REVERT: C 318 MET cc_start: 0.7977 (mpp) cc_final: 0.7495 (mpp) REVERT: C 534 MET cc_start: 0.8963 (tmm) cc_final: 0.8664 (tmm) REVERT: C 570 CYS cc_start: 0.8877 (m) cc_final: 0.8411 (m) REVERT: C 601 MET cc_start: 0.8169 (tmm) cc_final: 0.7901 (tmm) REVERT: C 677 TYR cc_start: 0.9203 (m-80) cc_final: 0.8827 (m-80) REVERT: D 118 LEU cc_start: 0.9064 (mm) cc_final: 0.8808 (tp) REVERT: D 125 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8786 (tp30) REVERT: D 207 ASP cc_start: 0.8812 (p0) cc_final: 0.8558 (p0) REVERT: D 318 MET cc_start: 0.7972 (mpp) cc_final: 0.7490 (mpp) REVERT: D 534 MET cc_start: 0.8968 (tmm) cc_final: 0.8672 (tmm) REVERT: D 570 CYS cc_start: 0.8854 (m) cc_final: 0.8398 (m) REVERT: D 601 MET cc_start: 0.8191 (tmm) cc_final: 0.7921 (tmm) REVERT: D 677 TYR cc_start: 0.9192 (m-80) cc_final: 0.8818 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3061 time to fit residues: 106.2098 Evaluate side-chains 172 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 166 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21048 Z= 0.251 Angle : 0.629 9.591 28484 Z= 0.313 Chirality : 0.041 0.150 3360 Planarity : 0.004 0.036 3696 Dihedral : 4.772 25.031 2912 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.68 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2708 helix: 0.89 (0.15), residues: 1300 sheet: -2.76 (0.22), residues: 468 loop : -1.89 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 304 HIS 0.003 0.001 HIS B 517 PHE 0.007 0.001 PHE D 178 TYR 0.010 0.001 TYR A 164 ARG 0.003 0.000 ARG C 551 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.340 Fit side-chains REVERT: A 118 LEU cc_start: 0.9082 (mm) cc_final: 0.8837 (tp) REVERT: A 119 MET cc_start: 0.8387 (tmm) cc_final: 0.8101 (tmm) REVERT: A 207 ASP cc_start: 0.8817 (p0) cc_final: 0.8561 (p0) REVERT: A 318 MET cc_start: 0.7989 (mpp) cc_final: 0.7535 (mpp) REVERT: A 534 MET cc_start: 0.8989 (tmm) cc_final: 0.8680 (tmm) REVERT: A 570 CYS cc_start: 0.8887 (m) cc_final: 0.8364 (m) REVERT: A 601 MET cc_start: 0.8125 (tmm) cc_final: 0.7699 (tmm) REVERT: A 677 TYR cc_start: 0.9226 (m-80) cc_final: 0.8872 (m-80) REVERT: B 118 LEU cc_start: 0.9083 (mm) cc_final: 0.8835 (tp) REVERT: B 119 MET cc_start: 0.8390 (tmm) cc_final: 0.8105 (tmm) REVERT: B 207 ASP cc_start: 0.8807 (p0) cc_final: 0.8555 (p0) REVERT: B 318 MET cc_start: 0.7936 (mpp) cc_final: 0.7474 (mpp) REVERT: B 534 MET cc_start: 0.8984 (tmm) cc_final: 0.8675 (tmm) REVERT: B 570 CYS cc_start: 0.8904 (m) cc_final: 0.8394 (m) REVERT: B 601 MET cc_start: 0.8122 (tmm) cc_final: 0.7701 (tmm) REVERT: B 677 TYR cc_start: 0.9238 (m-80) cc_final: 0.8877 (m-80) REVERT: C 118 LEU cc_start: 0.9087 (mm) cc_final: 0.8840 (tp) REVERT: C 119 MET cc_start: 0.8385 (tmm) cc_final: 0.8094 (tmm) REVERT: C 207 ASP cc_start: 0.8824 (p0) cc_final: 0.8568 (p0) REVERT: C 318 MET cc_start: 0.7937 (mpp) cc_final: 0.7485 (mpp) REVERT: C 534 MET cc_start: 0.8979 (tmm) cc_final: 0.8670 (tmm) REVERT: C 570 CYS cc_start: 0.8876 (m) cc_final: 0.8356 (m) REVERT: C 601 MET cc_start: 0.8115 (tmm) cc_final: 0.7690 (tmm) REVERT: C 677 TYR cc_start: 0.9215 (m-80) cc_final: 0.8867 (m-80) REVERT: D 118 LEU cc_start: 0.9080 (mm) cc_final: 0.8832 (tp) REVERT: D 119 MET cc_start: 0.8380 (tmm) cc_final: 0.8095 (tmm) REVERT: D 207 ASP cc_start: 0.8804 (p0) cc_final: 0.8548 (p0) REVERT: D 318 MET cc_start: 0.7935 (mpp) cc_final: 0.7479 (mpp) REVERT: D 534 MET cc_start: 0.8984 (tmm) cc_final: 0.8677 (tmm) REVERT: D 570 CYS cc_start: 0.8890 (m) cc_final: 0.8386 (m) REVERT: D 601 MET cc_start: 0.8135 (tmm) cc_final: 0.7712 (tmm) REVERT: D 677 TYR cc_start: 0.9205 (m-80) cc_final: 0.8858 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2712 time to fit residues: 94.5937 Evaluate side-chains 180 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 229 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 GLN ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21048 Z= 0.256 Angle : 0.629 8.987 28484 Z= 0.314 Chirality : 0.042 0.151 3360 Planarity : 0.004 0.037 3696 Dihedral : 4.792 25.246 2912 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.16 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2708 helix: 1.02 (0.15), residues: 1276 sheet: -2.74 (0.22), residues: 468 loop : -1.74 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 304 HIS 0.003 0.001 HIS B 517 PHE 0.007 0.001 PHE B 178 TYR 0.009 0.001 TYR A 164 ARG 0.003 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9055 (mm) cc_final: 0.8796 (tp) REVERT: A 119 MET cc_start: 0.8352 (tmm) cc_final: 0.8090 (tmm) REVERT: A 207 ASP cc_start: 0.8806 (p0) cc_final: 0.8560 (p0) REVERT: A 318 MET cc_start: 0.7875 (mpp) cc_final: 0.7404 (mpp) REVERT: A 534 MET cc_start: 0.8958 (tmm) cc_final: 0.8656 (tmm) REVERT: A 570 CYS cc_start: 0.8843 (m) cc_final: 0.8376 (m) REVERT: A 601 MET cc_start: 0.8088 (tmm) cc_final: 0.7834 (tmm) REVERT: A 677 TYR cc_start: 0.9203 (m-80) cc_final: 0.8857 (m-80) REVERT: B 118 LEU cc_start: 0.9056 (mm) cc_final: 0.8792 (tp) REVERT: B 119 MET cc_start: 0.8355 (tmm) cc_final: 0.8091 (tmm) REVERT: B 207 ASP cc_start: 0.8796 (p0) cc_final: 0.8556 (p0) REVERT: B 318 MET cc_start: 0.7862 (mpp) cc_final: 0.7392 (mpp) REVERT: B 534 MET cc_start: 0.8953 (tmm) cc_final: 0.8650 (tmm) REVERT: B 570 CYS cc_start: 0.8848 (m) cc_final: 0.8380 (m) REVERT: B 601 MET cc_start: 0.8085 (tmm) cc_final: 0.7831 (tmm) REVERT: B 677 TYR cc_start: 0.9215 (m-80) cc_final: 0.8861 (m-80) REVERT: C 118 LEU cc_start: 0.9059 (mm) cc_final: 0.8799 (tp) REVERT: C 119 MET cc_start: 0.8350 (tmm) cc_final: 0.8083 (tmm) REVERT: C 207 ASP cc_start: 0.8814 (p0) cc_final: 0.8567 (p0) REVERT: C 318 MET cc_start: 0.7868 (mpp) cc_final: 0.7404 (mpp) REVERT: C 534 MET cc_start: 0.8947 (tmm) cc_final: 0.8648 (tmm) REVERT: C 570 CYS cc_start: 0.8834 (m) cc_final: 0.8368 (m) REVERT: C 601 MET cc_start: 0.8078 (tmm) cc_final: 0.7827 (tmm) REVERT: C 677 TYR cc_start: 0.9191 (m-80) cc_final: 0.8852 (m-80) REVERT: D 118 LEU cc_start: 0.9052 (mm) cc_final: 0.8790 (tp) REVERT: D 119 MET cc_start: 0.8343 (tmm) cc_final: 0.8080 (tmm) REVERT: D 207 ASP cc_start: 0.8793 (p0) cc_final: 0.8551 (p0) REVERT: D 318 MET cc_start: 0.7863 (mpp) cc_final: 0.7398 (mpp) REVERT: D 534 MET cc_start: 0.8954 (tmm) cc_final: 0.8654 (tmm) REVERT: D 570 CYS cc_start: 0.8839 (m) cc_final: 0.8375 (m) REVERT: D 601 MET cc_start: 0.8099 (tmm) cc_final: 0.7846 (tmm) REVERT: D 677 TYR cc_start: 0.9181 (m-80) cc_final: 0.8843 (m-80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2959 time to fit residues: 101.4795 Evaluate side-chains 180 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 9.9990 chunk 258 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 270 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 639 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN D 639 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21048 Z= 0.353 Angle : 0.699 9.018 28484 Z= 0.352 Chirality : 0.043 0.144 3360 Planarity : 0.005 0.037 3696 Dihedral : 5.305 25.873 2912 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.64 % Favored : 89.22 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2708 helix: 0.69 (0.15), residues: 1284 sheet: -2.88 (0.21), residues: 468 loop : -1.97 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 304 HIS 0.005 0.001 HIS A 517 PHE 0.012 0.002 PHE B 178 TYR 0.014 0.002 TYR B 55 ARG 0.004 0.001 ARG A 551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.259 Fit side-chains REVERT: A 118 LEU cc_start: 0.9125 (mm) cc_final: 0.8861 (tp) REVERT: A 125 GLU cc_start: 0.9192 (tp30) cc_final: 0.8980 (tp30) REVERT: A 534 MET cc_start: 0.8906 (tmm) cc_final: 0.8648 (tmm) REVERT: A 570 CYS cc_start: 0.8843 (m) cc_final: 0.8384 (m) REVERT: A 601 MET cc_start: 0.8098 (tmm) cc_final: 0.7829 (tmm) REVERT: A 677 TYR cc_start: 0.9260 (m-80) cc_final: 0.8915 (m-80) REVERT: B 118 LEU cc_start: 0.9125 (mm) cc_final: 0.8859 (tp) REVERT: B 125 GLU cc_start: 0.9213 (tp30) cc_final: 0.8991 (tp30) REVERT: B 534 MET cc_start: 0.8901 (tmm) cc_final: 0.8644 (tmm) REVERT: B 570 CYS cc_start: 0.8841 (m) cc_final: 0.8388 (m) REVERT: B 601 MET cc_start: 0.8092 (tmm) cc_final: 0.7824 (tmm) REVERT: B 677 TYR cc_start: 0.9271 (m-80) cc_final: 0.8921 (m-80) REVERT: C 118 LEU cc_start: 0.9127 (mm) cc_final: 0.8865 (tp) REVERT: C 125 GLU cc_start: 0.9180 (tp30) cc_final: 0.8970 (tp30) REVERT: C 534 MET cc_start: 0.8896 (tmm) cc_final: 0.8641 (tmm) REVERT: C 570 CYS cc_start: 0.8830 (m) cc_final: 0.8376 (m) REVERT: C 601 MET cc_start: 0.8089 (tmm) cc_final: 0.7822 (tmm) REVERT: C 677 TYR cc_start: 0.9241 (m-80) cc_final: 0.8910 (m-80) REVERT: D 118 LEU cc_start: 0.9118 (mm) cc_final: 0.8857 (tp) REVERT: D 125 GLU cc_start: 0.9191 (tp30) cc_final: 0.8974 (tp30) REVERT: D 534 MET cc_start: 0.8901 (tmm) cc_final: 0.8645 (tmm) REVERT: D 570 CYS cc_start: 0.8836 (m) cc_final: 0.8381 (m) REVERT: D 601 MET cc_start: 0.8110 (tmm) cc_final: 0.7842 (tmm) REVERT: D 677 TYR cc_start: 0.9241 (m-80) cc_final: 0.8902 (m-80) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2765 time to fit residues: 86.6270 Evaluate side-chains 172 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 27 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064410 restraints weight = 77624.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067728 restraints weight = 57871.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066561 restraints weight = 55247.619| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21048 Z= 0.212 Angle : 0.628 9.801 28484 Z= 0.311 Chirality : 0.042 0.147 3360 Planarity : 0.004 0.035 3696 Dihedral : 4.829 24.983 2912 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.53 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2708 helix: 0.90 (0.15), residues: 1284 sheet: -2.71 (0.22), residues: 468 loop : -1.89 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 304 HIS 0.003 0.001 HIS A 607 PHE 0.015 0.001 PHE B 178 TYR 0.009 0.001 TYR D 55 ARG 0.003 0.000 ARG A 625 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3354.65 seconds wall clock time: 62 minutes 29.29 seconds (3749.29 seconds total)