Starting phenix.real_space_refine on Wed Aug 7 20:42:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/08_2024/7f5u_31467.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/08_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_31467/08_2024/7f5u_31467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/08_2024/7f5u_31467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/08_2024/7f5u_31467.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/08_2024/7f5u_31467.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.37, per 1000 atoms: 0.55 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: 8.66 Conformation dependent library (CDL) restraints added in 4.2 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: 2.53 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: 6.90 Time building geometry restraints manager: 9.42 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 3.040 nonbonded pdb=" O ALA A 509 " pdb=" OG1 THR A 512 " model vdw 2.101 3.040 nonbonded pdb=" O ALA B 509 " pdb=" OG1 THR B 512 " model vdw 2.101 3.040 nonbonded pdb=" O ALA D 509 " pdb=" OG1 THR D 512 " model vdw 2.101 3.040 nonbonded pdb=" O ASN D 672 " pdb=" OG1 THR D 676 " model vdw 2.159 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.220 Process input model: 56.480 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.020 ------------------------------------------------------------------------------- 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 : 2.403 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: 0.4294 time to fit residues: 161.8687 Evaluate side-chains 196 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.746 ------------------------------------------------------------------------------- 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: 8.9990 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 247 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 599 ASN A 675 HIS B 92 HIS B 354 ASN B 599 ASN B 675 HIS C 92 HIS C 599 ASN C 675 HIS D 92 HIS D 599 ASN D 675 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2420 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= 0.170 Angle : 0.629 8.222 28484 Z= 0.318 Chirality : 0.043 0.145 3360 Planarity : 0.004 0.038 3696 Dihedral : 4.809 24.489 2912 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.94 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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: -2.89 (0.16), residues: 2708 helix: -0.52 (0.14), residues: 1272 sheet: -3.84 (0.18), residues: 464 loop : -2.64 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 748 HIS 0.003 0.001 HIS B 272 PHE 0.015 0.001 PHE B 760 TYR 0.010 0.001 TYR A 157 ARG 0.005 0.001 ARG C 50 *********************** 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 312 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 207 ASP cc_start: 0.8817 (p0) cc_final: 0.8552 (p0) REVERT: A 271 MET cc_start: 0.6891 (tpp) cc_final: 0.6345 (tpp) REVERT: A 570 CYS cc_start: 0.8813 (m) cc_final: 0.8273 (m) REVERT: A 601 MET cc_start: 0.8135 (tmm) cc_final: 0.7665 (tmm) REVERT: A 605 LEU cc_start: 0.9421 (tp) cc_final: 0.9095 (mp) REVERT: B 90 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7729 (mm-30) REVERT: B 207 ASP cc_start: 0.8809 (p0) cc_final: 0.8546 (p0) REVERT: B 271 MET cc_start: 0.6904 (tpp) cc_final: 0.6346 (tpp) REVERT: B 570 CYS cc_start: 0.8819 (m) cc_final: 0.8280 (m) REVERT: B 601 MET cc_start: 0.8133 (tmm) cc_final: 0.7665 (tmm) REVERT: B 605 LEU cc_start: 0.9428 (tp) cc_final: 0.9107 (mp) REVERT: C 90 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7717 (mm-30) REVERT: C 207 ASP cc_start: 0.8827 (p0) cc_final: 0.8560 (p0) REVERT: C 271 MET cc_start: 0.6891 (tpp) cc_final: 0.6335 (tpp) REVERT: C 570 CYS cc_start: 0.8797 (m) cc_final: 0.8263 (m) REVERT: C 601 MET cc_start: 0.8126 (tmm) cc_final: 0.7658 (tmm) REVERT: C 605 LEU cc_start: 0.9412 (tp) cc_final: 0.9079 (mp) REVERT: D 90 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 207 ASP cc_start: 0.8807 (p0) cc_final: 0.8543 (p0) REVERT: D 271 MET cc_start: 0.6899 (tpp) cc_final: 0.6339 (tpp) REVERT: D 570 CYS cc_start: 0.8801 (m) cc_final: 0.8270 (m) REVERT: D 601 MET cc_start: 0.8149 (tmm) cc_final: 0.7681 (tmm) REVERT: D 605 LEU cc_start: 0.9413 (tp) cc_final: 0.9085 (mp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.3617 time to fit residues: 171.4190 Evaluate side-chains 224 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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: 9.9990 chunk 205 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 369 GLN A 375 ASN A 392 ASN A 565 HIS ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 375 ASN B 392 ASN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 HIS ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 369 GLN C 375 ASN C 392 ASN C 436 ASN C 565 HIS ** C 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 ASN D 369 GLN D 375 ASN D 392 ASN D 565 HIS ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2625 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: