Starting phenix.real_space_refine on Thu Aug 8 00:39:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zbg_6911/08_2024/5zbg_6911.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zbg_6911/08_2024/5zbg_6911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zbg_6911/08_2024/5zbg_6911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zbg_6911/08_2024/5zbg_6911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zbg_6911/08_2024/5zbg_6911.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zbg_6911/08_2024/5zbg_6911.cif" } resolution = 4.36 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= 0.021 sd= 0.092 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 124 5.16 5 C 13824 2.51 5 N 3460 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D ARG 540": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 21260 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5315 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 652} Chain breaks: 5 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5315 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 652} Chain breaks: 5 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5315 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 652} Chain breaks: 5 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5315 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 652} Chain breaks: 5 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 10.81, per 1000 atoms: 0.51 Number of scatterers: 21260 At special positions: 0 Unit cell: (127.41, 127.41, 167.14, 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 124 16.00 O 3852 8.00 N 3460 7.00 C 13824 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: 8.00 Conformation dependent library (CDL) restraints added in 3.7 seconds 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 3.657A pdb=" N TYR A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 removed outlier: 4.379A pdb=" N GLU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.659A pdb=" N ASN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 removed outlier: 3.693A pdb=" N LYS A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 102 through 111 removed outlier: 3.548A pdb=" N ASN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 4.069A pdb=" N GLU A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 141 " --> pdb=" O TYR A 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 141' Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.520A pdb=" N LYS A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 190 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 221 through 240 removed outlier: 4.287A pdb=" N THR A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.693A pdb=" N VAL A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.921A pdb=" N TYR A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 removed outlier: 3.914A pdb=" N CYS A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.922A pdb=" N LEU A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 369 through 393 Processing helix chain 'A' and resid 424 through 447 removed outlier: 3.795A pdb=" N LEU A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 removed outlier: 4.496A pdb=" N GLN A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 489 removed outlier: 3.563A pdb=" N LEU A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.536A pdb=" N ILE A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.527A pdb=" N LEU A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 587 removed outlier: 4.733A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 628 through 664 removed outlier: 3.503A pdb=" N GLU A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 683 Processing helix chain 'A' and resid 762 through 782 Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 788 through 828 removed outlier: 3.842A pdb=" N LEU A 792 " --> pdb=" O ASN A 788 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.657A pdb=" N TYR B 37 " --> pdb=" O ASP B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 50 removed outlier: 4.379A pdb=" N GLU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.659A pdb=" N ASN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 removed outlier: 3.693A pdb=" N LYS B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 102 through 111 removed outlier: 3.548A pdb=" N ASN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 removed outlier: 4.069A pdb=" N GLU B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 141 " --> pdb=" O TYR B 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 141' Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 160 through 170 removed outlier: 3.520A pdb=" N LYS B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 190 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 221 through 240 removed outlier: 4.287A pdb=" N THR B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 264 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 295 through 304 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.693A pdb=" N VAL B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.921A pdb=" N TYR B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.914A pdb=" N CYS B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 358 removed outlier: 3.922A pdb=" N LEU B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 369 through 393 Processing helix chain 'B' and resid 424 through 447 removed outlier: 3.795A pdb=" N LEU B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 455 removed outlier: 4.496A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 489 removed outlier: 3.563A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 540 removed outlier: 3.536A pdb=" N ILE B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 removed outlier: 3.527A pdb=" N LEU B 545 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 587 removed outlier: 4.733A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 628 through 664 removed outlier: 3.503A pdb=" N GLU B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 762 through 782 Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 788 through 828 removed outlier: 3.842A pdb=" N LEU B 792 " --> pdb=" O ASN B 788 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 37 removed outlier: 3.657A pdb=" N TYR C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 50 removed outlier: 4.379A pdb=" N GLU C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.659A pdb=" N ASN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.693A pdb=" N LYS C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.548A pdb=" N ASN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 removed outlier: 4.069A pdb=" N GLU C 140 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 141 " --> pdb=" O TYR C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 150 through 158 Processing helix chain 'C' and resid 160 through 170 removed outlier: 3.520A pdb=" N LYS C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 221 through 240 removed outlier: 4.287A pdb=" N THR C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 264 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.693A pdb=" N VAL C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.921A pdb=" N TYR C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 346 removed outlier: 3.914A pdb=" N CYS C 338 " --> pdb=" O ILE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 358 removed outlier: 3.922A pdb=" N LEU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 358 " --> pdb=" O GLY C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 369 through 393 Processing helix chain 'C' and resid 424 through 447 removed outlier: 3.795A pdb=" N LEU C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU C 447 " --> pdb=" O GLU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 455 removed outlier: 4.496A pdb=" N GLN C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 489 removed outlier: 3.563A pdb=" N LEU C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 540 removed outlier: 3.536A pdb=" N ILE C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 545 removed outlier: 3.527A pdb=" N LEU C 545 " --> pdb=" O ALA C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 587 removed outlier: 4.733A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 628 through 664 removed outlier: 3.503A pdb=" N GLU C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 683 Processing helix chain 'C' and resid 762 through 782 Processing helix chain 'C' and resid 783 through 785 No H-bonds generated for 'chain 'C' and resid 783 through 785' Processing helix chain 'C' and resid 788 through 828 removed outlier: 3.842A pdb=" N LEU C 792 " --> pdb=" O ASN C 788 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 removed outlier: 3.657A pdb=" N TYR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 50 removed outlier: 4.379A pdb=" N GLU D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.659A pdb=" N ASN D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 83 removed outlier: 3.693A pdb=" N LYS D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 102 through 111 removed outlier: 3.548A pdb=" N ASN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 141 removed outlier: 4.069A pdb=" N GLU D 140 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 141 " --> pdb=" O TYR D 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 141' Processing helix chain 'D' and resid 150 through 158 Processing helix chain 'D' and resid 160 through 170 removed outlier: 3.520A pdb=" N LYS D 170 " --> pdb=" O MET D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 190 Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 221 through 240 removed outlier: 4.287A pdb=" N THR D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 264 Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 295 through 304 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.693A pdb=" N VAL D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.921A pdb=" N TYR D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.914A pdb=" N CYS D 338 " --> pdb=" O ILE D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 358 removed outlier: 3.922A pdb=" N LEU D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 358 " --> pdb=" O GLY D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 Processing helix chain 'D' and resid 369 through 393 Processing helix chain 'D' and resid 424 through 447 removed outlier: 3.795A pdb=" N LEU D 446 " --> pdb=" O LYS D 442 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU D 447 " --> pdb=" O GLU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 4.496A pdb=" N GLN D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 489 removed outlier: 3.563A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 489 " --> pdb=" O ALA D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 540 removed outlier: 3.536A pdb=" N ILE D 532 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 545 removed outlier: 3.527A pdb=" N LEU D 545 " --> pdb=" O ALA D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 587 removed outlier: 4.733A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 628 through 664 removed outlier: 3.503A pdb=" N GLU D 664 " --> pdb=" O SER D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 683 Processing helix chain 'D' and resid 762 through 782 Processing helix chain 'D' and resid 783 through 785 No H-bonds generated for 'chain 'D' and resid 783 through 785' Processing helix chain 'D' and resid 788 through 828 removed outlier: 3.842A pdb=" N LEU D 792 " --> pdb=" O ASN D 788 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 4248 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: 6.14 Time building geometry restraints manager: 8.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6704 1.35 - 1.47: 5280 1.47 - 1.59: 9508 1.59 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 21696 Sorted by residual: bond pdb=" CA SER C 683 " pdb=" C SER C 683 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.72e-02 3.38e+03 5.64e+00 bond pdb=" CA SER D 683 " pdb=" C SER D 683 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.72e-02 3.38e+03 5.64e+00 bond pdb=" CA SER A 683 " pdb=" C SER A 683 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.72e-02 3.38e+03 5.64e+00 bond pdb=" CA SER B 683 " pdb=" C SER B 683 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.72e-02 3.38e+03 5.64e+00 bond pdb=" C ALA B 310 " pdb=" N HIS B 311 " ideal model delta sigma weight residual 1.340 1.225 0.115 5.87e-02 2.90e+02 3.86e+00 ... (remaining 21691 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.60: 444 106.60 - 113.50: 12144 113.50 - 120.39: 8636 120.39 - 127.28: 7924 127.28 - 134.18: 192 Bond angle restraints: 29340 Sorted by residual: angle pdb=" CA TRP C 681 " pdb=" CB TRP C 681 " pdb=" CG TRP C 681 " ideal model delta sigma weight residual 113.60 122.17 -8.57 1.90e+00 2.77e-01 2.03e+01 angle pdb=" CA TRP D 681 " pdb=" CB TRP D 681 " pdb=" CG TRP D 681 " ideal model delta sigma weight residual 113.60 122.17 -8.57 1.90e+00 2.77e-01 2.03e+01 angle pdb=" CA TRP B 681 " pdb=" CB TRP B 681 " pdb=" CG TRP B 681 " ideal model delta sigma weight residual 113.60 122.17 -8.57 1.90e+00 2.77e-01 2.03e+01 angle pdb=" CA TRP A 681 " pdb=" CB TRP A 681 " pdb=" CG TRP A 681 " ideal model delta sigma weight residual 113.60 122.17 -8.57 1.90e+00 2.77e-01 2.03e+01 angle pdb=" C LEU A 680 " pdb=" N TRP A 681 " pdb=" CA TRP A 681 " ideal model delta sigma weight residual 122.65 116.33 6.32 1.66e+00 3.63e-01 1.45e+01 ... (remaining 29335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 11764 17.39 - 34.79: 892 34.79 - 52.18: 244 52.18 - 69.57: 40 69.57 - 86.97: 16 Dihedral angle restraints: 12956 sinusoidal: 5076 harmonic: 7880 Sorted by residual: dihedral pdb=" CA PHE A 145 " pdb=" C PHE A 145 " pdb=" N SER A 146 " pdb=" CA SER A 146 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE D 145 " pdb=" C PHE D 145 " pdb=" N SER D 146 " pdb=" CA SER D 146 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE C 145 " pdb=" C PHE C 145 " pdb=" N SER C 146 " pdb=" CA SER C 146 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 12953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2352 0.039 - 0.078: 828 0.078 - 0.117: 136 0.117 - 0.157: 16 0.157 - 0.196: 8 Chirality restraints: 3340 Sorted by residual: chirality pdb=" CA TRP B 681 " pdb=" N TRP B 681 " pdb=" C TRP B 681 " pdb=" CB TRP B 681 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA TRP C 681 " pdb=" N TRP C 681 " pdb=" C TRP C 681 " pdb=" CB TRP C 681 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA TRP A 681 " pdb=" N TRP A 681 " pdb=" C TRP A 681 " pdb=" CB TRP A 681 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 3337 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 627 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C ASP D 627 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP D 627 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS D 628 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 627 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C ASP C 627 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP C 627 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS C 628 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 627 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C ASP A 627 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 627 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 628 " 0.010 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4984 2.79 - 3.31: 20804 3.31 - 3.84: 34092 3.84 - 4.37: 36554 4.37 - 4.90: 62656 Nonbonded interactions: 159090 Sorted by model distance: nonbonded pdb=" N PHE A 599 " pdb=" OE2 GLU A 604 " model vdw 2.258 3.120 nonbonded pdb=" N PHE D 599 " pdb=" OE2 GLU D 604 " model vdw 2.258 3.120 nonbonded pdb=" N PHE B 599 " pdb=" OE2 GLU B 604 " model vdw 2.258 3.120 nonbonded pdb=" N PHE C 599 " pdb=" OE2 GLU C 604 " model vdw 2.258 3.120 nonbonded pdb=" NZ LYS A 594 " pdb=" O SER A 621 " model vdw 2.279 3.120 ... (remaining 159085 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: 0.480 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: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 52.530 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.005 0.115 21696 Z= 0.314 Angle : 0.697 8.569 29340 Z= 0.378 Chirality : 0.039 0.196 3340 Planarity : 0.004 0.039 3668 Dihedral : 13.892 86.965 7844 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.99 % Favored : 92.71 % Rotamer: Outliers : 4.79 % Allowed : 11.52 % Favored : 83.69 % 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: -2.22 (0.14), residues: 2632 helix: -0.55 (0.10), residues: 1968 sheet: None (None), residues: 0 loop : -4.18 (0.17), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 681 HIS 0.004 0.001 HIS A 198 PHE 0.014 0.002 PHE B 577 TYR 0.016 0.002 TYR D 136 ARG 0.002 0.000 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 564 time to evaluate : 2.432 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 40 ILE cc_start: 0.9838 (OUTLIER) cc_final: 0.9520 (pt) REVERT: A 144 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.9084 (ptp-170) REVERT: A 154 LEU cc_start: 0.9833 (tp) cc_final: 0.9578 (tt) REVERT: A 158 CYS cc_start: 0.9284 (m) cc_final: 0.8569 (t) REVERT: A 160 LYS cc_start: 0.9294 (mmtt) cc_final: 0.8280 (mmtp) REVERT: A 188 MET cc_start: 0.9635 (ttp) cc_final: 0.9341 (tmm) REVERT: A 228 GLU cc_start: 0.9628 (tt0) cc_final: 0.9253 (tm-30) REVERT: A 232 GLU cc_start: 0.9488 (tt0) cc_final: 0.9204 (tp30) REVERT: A 252 MET cc_start: 0.9668 (ttp) cc_final: 0.8946 (ppp) REVERT: A 264 LEU cc_start: 0.9756 (tp) cc_final: 0.9519 (tt) REVERT: A 301 ILE cc_start: 0.9618 (pt) cc_final: 0.9400 (mm) REVERT: A 427 MET cc_start: 0.9042 (mtp) cc_final: 0.8605 (mmt) REVERT: A 432 TRP cc_start: 0.9355 (t-100) cc_final: 0.8764 (t-100) REVERT: A 437 MET cc_start: 0.9467 (ttp) cc_final: 0.9248 (tpp) REVERT: A 440 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8909 (tp30) REVERT: A 564 ASP cc_start: 0.8936 (m-30) cc_final: 0.8425 (t70) REVERT: A 568 PHE cc_start: 0.9529 (m-80) cc_final: 0.9033 (m-10) REVERT: A 604 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: A 609 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9338 (tt) REVERT: A 632 GLU cc_start: 0.9284 (tt0) cc_final: 0.8760 (tp30) REVERT: A 650 LEU cc_start: 0.9710 (mm) cc_final: 0.9290 (tt) REVERT: A 654 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9585 (mp) REVERT: A 657 MET cc_start: 0.9465 (mmm) cc_final: 0.9154 (tmm) REVERT: A 658 ILE cc_start: 0.9696 (mt) cc_final: 0.9357 (mt) REVERT: A 672 GLU cc_start: 0.9633 (mt-10) cc_final: 0.9321 (mm-30) REVERT: A 779 GLN cc_start: 0.9701 (tt0) cc_final: 0.9156 (tm-30) REVERT: A 781 ASP cc_start: 0.9488 (m-30) cc_final: 0.9263 (t0) REVERT: A 782 LYS cc_start: 0.9417 (ttpt) cc_final: 0.9200 (tppt) REVERT: A 783 GLU cc_start: 0.9572 (mt-10) cc_final: 0.9127 (mp0) REVERT: B 40 ILE cc_start: 0.9837 (OUTLIER) cc_final: 0.9520 (pt) REVERT: B 144 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.9084 (ptp-170) REVERT: B 154 LEU cc_start: 0.9833 (tp) cc_final: 0.9578 (tt) REVERT: B 158 CYS cc_start: 0.9283 (m) cc_final: 0.8568 (t) REVERT: B 160 LYS cc_start: 0.9293 (mmtt) cc_final: 0.8277 (mmtp) REVERT: B 188 MET cc_start: 0.9634 (ttp) cc_final: 0.9342 (tmm) REVERT: B 228 GLU cc_start: 0.9628 (tt0) cc_final: 0.9253 (tm-30) REVERT: B 232 GLU cc_start: 0.9489 (tt0) cc_final: 0.9205 (tp30) REVERT: B 252 MET cc_start: 0.9669 (ttp) cc_final: 0.8946 (ppp) REVERT: B 264 LEU cc_start: 0.9756 (tp) cc_final: 0.9519 (tt) REVERT: B 301 ILE cc_start: 0.9617 (pt) cc_final: 0.9399 (mm) REVERT: B 427 MET cc_start: 0.9042 (mtp) cc_final: 0.8605 (mmt) REVERT: B 432 TRP cc_start: 0.9356 (t-100) cc_final: 0.8764 (t-100) REVERT: B 437 MET cc_start: 0.9466 (ttp) cc_final: 0.9248 (tpp) REVERT: B 440 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8909 (tp30) REVERT: B 564 ASP cc_start: 0.8936 (m-30) cc_final: 0.8425 (t70) REVERT: B 568 PHE cc_start: 0.9530 (m-80) cc_final: 0.9033 (m-10) REVERT: B 604 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: B 609 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9339 (tt) REVERT: B 632 GLU cc_start: 0.9284 (tt0) cc_final: 0.8758 (tp30) REVERT: B 650 LEU cc_start: 0.9711 (mm) cc_final: 0.9291 (tt) REVERT: B 654 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9585 (mp) REVERT: B 657 MET cc_start: 0.9467 (mmm) cc_final: 0.9154 (tmm) REVERT: B 658 ILE cc_start: 0.9696 (mt) cc_final: 0.9359 (mt) REVERT: B 672 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9320 (mm-30) REVERT: B 779 GLN cc_start: 0.9700 (tt0) cc_final: 0.9157 (tm-30) REVERT: B 781 ASP cc_start: 0.9487 (m-30) cc_final: 0.9264 (t0) REVERT: B 782 LYS cc_start: 0.9418 (ttpt) cc_final: 0.9199 (tppt) REVERT: B 783 GLU cc_start: 0.9573 (mt-10) cc_final: 0.9128 (mp0) REVERT: C 40 ILE cc_start: 0.9837 (OUTLIER) cc_final: 0.9519 (pt) REVERT: C 144 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.9083 (ptp-170) REVERT: C 154 LEU cc_start: 0.9832 (tp) cc_final: 0.9577 (tt) REVERT: C 158 CYS cc_start: 0.9285 (m) cc_final: 0.8570 (t) REVERT: C 160 LYS cc_start: 0.9294 (mmtt) cc_final: 0.8279 (mmtp) REVERT: C 188 MET cc_start: 0.9635 (ttp) cc_final: 0.9342 (tmm) REVERT: C 228 GLU cc_start: 0.9628 (tt0) cc_final: 0.9252 (tm-30) REVERT: C 232 GLU cc_start: 0.9488 (tt0) cc_final: 0.9204 (tp30) REVERT: C 252 MET cc_start: 0.9669 (ttp) cc_final: 0.8945 (ppp) REVERT: C 264 LEU cc_start: 0.9755 (tp) cc_final: 0.9520 (tt) REVERT: C 301 ILE cc_start: 0.9618 (pt) cc_final: 0.9400 (mm) REVERT: C 427 MET cc_start: 0.9042 (mtp) cc_final: 0.8605 (mmt) REVERT: C 432 TRP cc_start: 0.9357 (t-100) cc_final: 0.8764 (t-100) REVERT: C 437 MET cc_start: 0.9467 (ttp) cc_final: 0.9248 (tpp) REVERT: C 440 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8908 (tp30) REVERT: C 564 ASP cc_start: 0.8935 (m-30) cc_final: 0.8425 (t70) REVERT: C 568 PHE cc_start: 0.9530 (m-80) cc_final: 0.9035 (m-10) REVERT: C 604 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: C 609 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9338 (tt) REVERT: C 632 GLU cc_start: 0.9284 (tt0) cc_final: 0.8759 (tp30) REVERT: C 650 LEU cc_start: 0.9710 (mm) cc_final: 0.9291 (tt) REVERT: C 654 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9584 (mp) REVERT: C 657 MET cc_start: 0.9467 (mmm) cc_final: 0.9155 (tmm) REVERT: C 658 ILE cc_start: 0.9696 (mt) cc_final: 0.9358 (mt) REVERT: C 672 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9320 (mm-30) REVERT: C 779 GLN cc_start: 0.9700 (tt0) cc_final: 0.9156 (tm-30) REVERT: C 781 ASP cc_start: 0.9489 (m-30) cc_final: 0.9264 (t0) REVERT: C 782 LYS cc_start: 0.9418 (ttpt) cc_final: 0.9200 (tppt) REVERT: C 783 GLU cc_start: 0.9574 (mt-10) cc_final: 0.9127 (mp0) REVERT: D 40 ILE cc_start: 0.9838 (OUTLIER) cc_final: 0.9519 (pt) REVERT: D 144 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.9083 (ptp-170) REVERT: D 154 LEU cc_start: 0.9832 (tp) cc_final: 0.9577 (tt) REVERT: D 158 CYS cc_start: 0.9285 (m) cc_final: 0.8567 (t) REVERT: D 160 LYS cc_start: 0.9294 (mmtt) cc_final: 0.8277 (mmtp) REVERT: D 188 MET cc_start: 0.9634 (ttp) cc_final: 0.9341 (tmm) REVERT: D 228 GLU cc_start: 0.9627 (tt0) cc_final: 0.9252 (tm-30) REVERT: D 232 GLU cc_start: 0.9488 (tt0) cc_final: 0.9206 (tp30) REVERT: D 252 MET cc_start: 0.9669 (ttp) cc_final: 0.8946 (ppp) REVERT: D 264 LEU cc_start: 0.9755 (tp) cc_final: 0.9519 (tt) REVERT: D 301 ILE cc_start: 0.9618 (pt) cc_final: 0.9400 (mm) REVERT: D 427 MET cc_start: 0.9043 (mtp) cc_final: 0.8606 (mmt) REVERT: D 432 TRP cc_start: 0.9356 (t-100) cc_final: 0.8765 (t-100) REVERT: D 437 MET cc_start: 0.9466 (ttp) cc_final: 0.9248 (tpp) REVERT: D 440 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8909 (tp30) REVERT: D 564 ASP cc_start: 0.8936 (m-30) cc_final: 0.8425 (t70) REVERT: D 568 PHE cc_start: 0.9530 (m-80) cc_final: 0.9031 (m-10) REVERT: D 604 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: D 609 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9338 (tt) REVERT: D 632 GLU cc_start: 0.9284 (tt0) cc_final: 0.8759 (tp30) REVERT: D 650 LEU cc_start: 0.9710 (mm) cc_final: 0.9290 (tt) REVERT: D 654 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9584 (mp) REVERT: D 657 MET cc_start: 0.9465 (mmm) cc_final: 0.9155 (tmm) REVERT: D 658 ILE cc_start: 0.9696 (mt) cc_final: 0.9357 (mt) REVERT: D 672 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9319 (mm-30) REVERT: D 779 GLN cc_start: 0.9700 (tt0) cc_final: 0.9157 (tm-30) REVERT: D 781 ASP cc_start: 0.9488 (m-30) cc_final: 0.9263 (t0) REVERT: D 782 LYS cc_start: 0.9417 (ttpt) cc_final: 0.9200 (tppt) REVERT: D 783 GLU cc_start: 0.9573 (mt-10) cc_final: 0.9127 (mp0) outliers start: 108 outliers final: 28 residues processed: 656 average time/residue: 0.3001 time to fit residues: 311.1296 Evaluate side-chains 433 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 385 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 127 optimal weight: 0.1980 chunk 156 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 276 ASN C 276 ASN D 276 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21696 Z= 0.205 Angle : 0.627 7.578 29340 Z= 0.323 Chirality : 0.039 0.168 3340 Planarity : 0.004 0.042 3668 Dihedral : 4.384 18.757 2872 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 0.11 (0.16), residues: 2632 helix: 1.20 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -3.63 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 356 HIS 0.004 0.001 HIS B 311 PHE 0.011 0.001 PHE D 576 TYR 0.017 0.002 TYR D 662 ARG 0.004 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 CYS cc_start: 0.8785 (m) cc_final: 0.8542 (m) REVERT: A 160 LYS cc_start: 0.9192 (mmtt) cc_final: 0.8838 (mmtp) REVERT: A 166 MET cc_start: 0.9603 (mmp) cc_final: 0.9356 (mmp) REVERT: A 188 MET cc_start: 0.9641 (ttp) cc_final: 0.9329 (tmm) REVERT: A 252 MET cc_start: 0.9493 (ttp) cc_final: 0.8880 (ppp) REVERT: A 256 ASP cc_start: 0.9415 (m-30) cc_final: 0.8925 (m-30) REVERT: A 299 LEU cc_start: 0.9789 (tp) cc_final: 0.9566 (tt) REVERT: A 427 MET cc_start: 0.9038 (mtp) cc_final: 0.8782 (ptp) REVERT: A 440 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8635 (tp30) REVERT: A 464 MET cc_start: 0.9360 (ppp) cc_final: 0.9036 (ppp) REVERT: A 529 LEU cc_start: 0.9739 (mt) cc_final: 0.9531 (mt) REVERT: A 545 LEU cc_start: 0.9720 (tp) cc_final: 0.9501 (tp) REVERT: A 564 ASP cc_start: 0.8925 (m-30) cc_final: 0.8571 (t70) REVERT: A 650 LEU cc_start: 0.9702 (mm) cc_final: 0.9276 (tt) REVERT: A 657 MET cc_start: 0.9428 (mmm) cc_final: 0.9202 (mmm) REVERT: A 672 GLU cc_start: 0.9562 (mt-10) cc_final: 0.9359 (mm-30) REVERT: A 779 GLN cc_start: 0.9680 (tt0) cc_final: 0.9248 (tm-30) REVERT: B 158 CYS cc_start: 0.8783 (m) cc_final: 0.8539 (m) REVERT: B 160 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8835 (mmtp) REVERT: B 166 MET cc_start: 0.9603 (mmp) cc_final: 0.9356 (mmp) REVERT: B 188 MET cc_start: 0.9642 (ttp) cc_final: 0.9330 (tmm) REVERT: B 252 MET cc_start: 0.9493 (ttp) cc_final: 0.8881 (ppp) REVERT: B 256 ASP cc_start: 0.9414 (m-30) cc_final: 0.8926 (m-30) REVERT: B 299 LEU cc_start: 0.9788 (tp) cc_final: 0.9566 (tt) REVERT: B 427 MET cc_start: 0.9038 (mtp) cc_final: 0.8782 (ptp) REVERT: B 440 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8635 (tp30) REVERT: B 464 MET cc_start: 0.9361 (ppp) cc_final: 0.9037 (ppp) REVERT: B 529 LEU cc_start: 0.9740 (mt) cc_final: 0.9532 (mt) REVERT: B 545 LEU cc_start: 0.9720 (tp) cc_final: 0.9501 (tp) REVERT: B 564 ASP cc_start: 0.8925 (m-30) cc_final: 0.8427 (t70) REVERT: B 568 PHE cc_start: 0.9461 (m-80) cc_final: 0.8738 (m-80) REVERT: B 650 LEU cc_start: 0.9702 (mm) cc_final: 0.9269 (tt) REVERT: B 654 LEU cc_start: 0.9819 (mp) cc_final: 0.9522 (mp) REVERT: B 657 MET cc_start: 0.9428 (mmm) cc_final: 0.8958 (tmm) REVERT: B 658 ILE cc_start: 0.9607 (mt) cc_final: 0.9284 (mt) REVERT: B 672 GLU cc_start: 0.9562 (mt-10) cc_final: 0.9359 (mm-30) REVERT: B 779 GLN cc_start: 0.9680 (tt0) cc_final: 0.9249 (tm-30) REVERT: C 158 CYS cc_start: 0.8782 (m) cc_final: 0.8543 (m) REVERT: C 160 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8839 (mmtp) REVERT: C 166 MET cc_start: 0.9603 (mmp) cc_final: 0.9356 (mmp) REVERT: C 188 MET cc_start: 0.9641 (ttp) cc_final: 0.9328 (tmm) REVERT: C 252 MET cc_start: 0.9493 (ttp) cc_final: 0.8881 (ppp) REVERT: C 256 ASP cc_start: 0.9414 (m-30) cc_final: 0.8925 (m-30) REVERT: C 299 LEU cc_start: 0.9788 (tp) cc_final: 0.9567 (tt) REVERT: C 427 MET cc_start: 0.9038 (mtp) cc_final: 0.8782 (ptp) REVERT: C 440 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8634 (tp30) REVERT: C 464 MET cc_start: 0.9362 (ppp) cc_final: 0.9038 (ppp) REVERT: C 529 LEU cc_start: 0.9740 (mt) cc_final: 0.9532 (mt) REVERT: C 545 LEU cc_start: 0.9720 (tp) cc_final: 0.9500 (tp) REVERT: C 564 ASP cc_start: 0.8925 (m-30) cc_final: 0.8425 (t70) REVERT: C 568 PHE cc_start: 0.9461 (m-80) cc_final: 0.8736 (m-80) REVERT: C 650 LEU cc_start: 0.9701 (mm) cc_final: 0.9269 (tt) REVERT: C 654 LEU cc_start: 0.9819 (mp) cc_final: 0.9520 (mp) REVERT: C 657 MET cc_start: 0.9427 (mmm) cc_final: 0.8955 (tmm) REVERT: C 658 ILE cc_start: 0.9606 (mt) cc_final: 0.9282 (mt) REVERT: C 672 GLU cc_start: 0.9562 (mt-10) cc_final: 0.9358 (mm-30) REVERT: C 779 GLN cc_start: 0.9680 (tt0) cc_final: 0.9249 (tm-30) REVERT: D 158 CYS cc_start: 0.8830 (m) cc_final: 0.8585 (m) REVERT: D 160 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8894 (mmtp) REVERT: D 166 MET cc_start: 0.9615 (mmp) cc_final: 0.9368 (mmp) REVERT: D 188 MET cc_start: 0.9641 (ttp) cc_final: 0.9329 (tmm) REVERT: D 252 MET cc_start: 0.9493 (ttp) cc_final: 0.8880 (ppp) REVERT: D 256 ASP cc_start: 0.9415 (m-30) cc_final: 0.8924 (m-30) REVERT: D 299 LEU cc_start: 0.9788 (tp) cc_final: 0.9566 (tt) REVERT: D 427 MET cc_start: 0.9039 (mtp) cc_final: 0.8782 (ptp) REVERT: D 440 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8635 (tp30) REVERT: D 464 MET cc_start: 0.9361 (ppp) cc_final: 0.9037 (ppp) REVERT: D 529 LEU cc_start: 0.9739 (mt) cc_final: 0.9531 (mt) REVERT: D 545 LEU cc_start: 0.9720 (tp) cc_final: 0.9503 (tp) REVERT: D 564 ASP cc_start: 0.8924 (m-30) cc_final: 0.8427 (t70) REVERT: D 568 PHE cc_start: 0.9460 (m-80) cc_final: 0.8734 (m-80) REVERT: D 650 LEU cc_start: 0.9701 (mm) cc_final: 0.9270 (tt) REVERT: D 654 LEU cc_start: 0.9818 (mp) cc_final: 0.9520 (mp) REVERT: D 657 MET cc_start: 0.9428 (mmm) cc_final: 0.8954 (tmm) REVERT: D 658 ILE cc_start: 0.9606 (mt) cc_final: 0.9288 (mt) REVERT: D 672 GLU cc_start: 0.9562 (mt-10) cc_final: 0.9358 (mm-30) REVERT: D 779 GLN cc_start: 0.9680 (tt0) cc_final: 0.9248 (tm-30) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.2933 time to fit residues: 199.1990 Evaluate side-chains 322 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 165 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 263 optimal weight: 8.9990 chunk 217 optimal weight: 0.6980 chunk 241 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21696 Z= 0.151 Angle : 0.560 8.337 29340 Z= 0.291 Chirality : 0.037 0.155 3340 Planarity : 0.004 0.046 3668 Dihedral : 4.186 22.349 2872 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.18 % Allowed : 1.60 % Favored : 98.23 % 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: 0.92 (0.17), residues: 2632 helix: 1.71 (0.12), residues: 2024 sheet: None (None), residues: 0 loop : -3.40 (0.20), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 681 HIS 0.003 0.000 HIS B 311 PHE 0.017 0.001 PHE A 468 TYR 0.020 0.001 TYR D 138 ARG 0.002 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 430 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 CYS cc_start: 0.8721 (m) cc_final: 0.8340 (m) REVERT: A 160 LYS cc_start: 0.9171 (mmtt) cc_final: 0.8579 (mmtp) REVERT: A 169 MET cc_start: 0.9482 (tpp) cc_final: 0.9028 (mmm) REVERT: A 188 MET cc_start: 0.9629 (ttp) cc_final: 0.9329 (tmm) REVERT: A 252 MET cc_start: 0.9432 (ttp) cc_final: 0.8801 (ppp) REVERT: A 256 ASP cc_start: 0.9367 (m-30) cc_final: 0.9015 (m-30) REVERT: A 314 CYS cc_start: 0.9493 (t) cc_final: 0.9143 (t) REVERT: A 427 MET cc_start: 0.8973 (mtp) cc_final: 0.8642 (ptp) REVERT: A 441 CYS cc_start: 0.9053 (t) cc_final: 0.8747 (p) REVERT: A 464 MET cc_start: 0.9193 (ppp) cc_final: 0.8855 (ppp) REVERT: A 545 LEU cc_start: 0.9692 (tp) cc_final: 0.9468 (tp) REVERT: A 564 ASP cc_start: 0.8730 (m-30) cc_final: 0.8348 (t70) REVERT: A 568 PHE cc_start: 0.9230 (m-10) cc_final: 0.8254 (m-10) REVERT: A 580 MET cc_start: 0.9594 (tmm) cc_final: 0.9368 (tmm) REVERT: A 650 LEU cc_start: 0.9689 (mm) cc_final: 0.9353 (tt) REVERT: A 658 ILE cc_start: 0.9510 (mt) cc_final: 0.9052 (mm) REVERT: A 672 GLU cc_start: 0.9647 (mt-10) cc_final: 0.9336 (mm-30) REVERT: B 158 CYS cc_start: 0.8720 (m) cc_final: 0.8339 (m) REVERT: B 160 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8579 (mmtp) REVERT: B 169 MET cc_start: 0.9482 (tpp) cc_final: 0.9028 (mmm) REVERT: B 188 MET cc_start: 0.9629 (ttp) cc_final: 0.9328 (tmm) REVERT: B 252 MET cc_start: 0.9432 (ttp) cc_final: 0.8801 (ppp) REVERT: B 256 ASP cc_start: 0.9366 (m-30) cc_final: 0.9014 (m-30) REVERT: B 314 CYS cc_start: 0.9495 (t) cc_final: 0.9144 (t) REVERT: B 427 MET cc_start: 0.8973 (mtp) cc_final: 0.8642 (ptp) REVERT: B 441 CYS cc_start: 0.9053 (t) cc_final: 0.8747 (p) REVERT: B 464 MET cc_start: 0.9195 (ppp) cc_final: 0.8856 (ppp) REVERT: B 545 LEU cc_start: 0.9693 (tp) cc_final: 0.9467 (tp) REVERT: B 564 ASP cc_start: 0.8823 (m-30) cc_final: 0.8433 (t70) REVERT: B 580 MET cc_start: 0.9595 (tmm) cc_final: 0.9368 (tmm) REVERT: B 650 LEU cc_start: 0.9698 (mm) cc_final: 0.9219 (tt) REVERT: B 672 GLU cc_start: 0.9645 (mt-10) cc_final: 0.9335 (mm-30) REVERT: C 158 CYS cc_start: 0.8721 (m) cc_final: 0.8339 (m) REVERT: C 160 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8580 (mmtp) REVERT: C 169 MET cc_start: 0.9482 (tpp) cc_final: 0.9028 (mmm) REVERT: C 188 MET cc_start: 0.9630 (ttp) cc_final: 0.9328 (tmm) REVERT: C 252 MET cc_start: 0.9431 (ttp) cc_final: 0.8800 (ppp) REVERT: C 256 ASP cc_start: 0.9366 (m-30) cc_final: 0.9015 (m-30) REVERT: C 314 CYS cc_start: 0.9495 (t) cc_final: 0.9145 (t) REVERT: C 427 MET cc_start: 0.8973 (mtp) cc_final: 0.8641 (ptp) REVERT: C 441 CYS cc_start: 0.9052 (t) cc_final: 0.8747 (p) REVERT: C 464 MET cc_start: 0.9196 (ppp) cc_final: 0.8857 (ppp) REVERT: C 545 LEU cc_start: 0.9692 (tp) cc_final: 0.9467 (tp) REVERT: C 564 ASP cc_start: 0.8822 (m-30) cc_final: 0.8435 (t70) REVERT: C 580 MET cc_start: 0.9595 (tmm) cc_final: 0.9368 (tmm) REVERT: C 650 LEU cc_start: 0.9699 (mm) cc_final: 0.9219 (tt) REVERT: C 672 GLU cc_start: 0.9646 (mt-10) cc_final: 0.9335 (mm-30) REVERT: D 158 CYS cc_start: 0.8731 (m) cc_final: 0.8359 (m) REVERT: D 160 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8595 (mmtp) REVERT: D 169 MET cc_start: 0.9538 (tpp) cc_final: 0.9068 (mmm) REVERT: D 188 MET cc_start: 0.9629 (ttp) cc_final: 0.9329 (tmm) REVERT: D 252 MET cc_start: 0.9434 (ttp) cc_final: 0.8804 (ppp) REVERT: D 256 ASP cc_start: 0.9368 (m-30) cc_final: 0.9018 (m-30) REVERT: D 314 CYS cc_start: 0.9494 (t) cc_final: 0.9141 (t) REVERT: D 427 MET cc_start: 0.8973 (mtp) cc_final: 0.8642 (ptp) REVERT: D 441 CYS cc_start: 0.9053 (t) cc_final: 0.8747 (p) REVERT: D 464 MET cc_start: 0.9196 (ppp) cc_final: 0.8857 (ppp) REVERT: D 545 LEU cc_start: 0.9692 (tp) cc_final: 0.9466 (tp) REVERT: D 558 LEU cc_start: 0.9659 (mt) cc_final: 0.9432 (mt) REVERT: D 564 ASP cc_start: 0.8819 (m-30) cc_final: 0.8419 (t70) REVERT: D 580 MET cc_start: 0.9594 (tmm) cc_final: 0.9367 (tmm) REVERT: D 650 LEU cc_start: 0.9698 (mm) cc_final: 0.9218 (tt) REVERT: D 672 GLU cc_start: 0.9646 (mt-10) cc_final: 0.9335 (mm-30) outliers start: 4 outliers final: 0 residues processed: 434 average time/residue: 0.2970 time to fit residues: 208.4475 Evaluate side-chains 324 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 21696 Z= 0.382 Angle : 0.754 10.465 29340 Z= 0.390 Chirality : 0.041 0.208 3340 Planarity : 0.005 0.056 3668 Dihedral : 4.857 22.208 2872 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 0.80 (0.17), residues: 2632 helix: 1.67 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -3.31 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 681 HIS 0.013 0.002 HIS C 311 PHE 0.018 0.002 PHE D 15 TYR 0.020 0.003 TYR D 662 ARG 0.006 0.001 ARG C 266 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 CYS cc_start: 0.9000 (m) cc_final: 0.8725 (m) REVERT: A 160 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8992 (mmtp) REVERT: A 169 MET cc_start: 0.9459 (tpp) cc_final: 0.9075 (mmm) REVERT: A 188 MET cc_start: 0.9672 (ttp) cc_final: 0.9216 (mmm) REVERT: A 252 MET cc_start: 0.9462 (ttp) cc_final: 0.9180 (ttm) REVERT: A 253 GLN cc_start: 0.9429 (pt0) cc_final: 0.9112 (pp30) REVERT: A 427 MET cc_start: 0.8953 (mtp) cc_final: 0.8637 (ptp) REVERT: A 441 CYS cc_start: 0.9145 (t) cc_final: 0.8786 (p) REVERT: A 464 MET cc_start: 0.9267 (ppp) cc_final: 0.8962 (ppp) REVERT: A 545 LEU cc_start: 0.9720 (tp) cc_final: 0.9512 (tp) REVERT: A 569 MET cc_start: 0.9147 (ttm) cc_final: 0.8636 (mtp) REVERT: A 583 MET cc_start: 0.9621 (mmt) cc_final: 0.9187 (mmm) REVERT: A 650 LEU cc_start: 0.9649 (mm) cc_final: 0.9253 (tt) REVERT: A 654 LEU cc_start: 0.9741 (mp) cc_final: 0.9430 (mp) REVERT: A 657 MET cc_start: 0.8967 (ppp) cc_final: 0.8687 (ppp) REVERT: A 668 ASP cc_start: 0.8738 (m-30) cc_final: 0.8354 (m-30) REVERT: A 672 GLU cc_start: 0.9747 (mt-10) cc_final: 0.9431 (mm-30) REVERT: B 61 MET cc_start: 0.9534 (mmp) cc_final: 0.9300 (mmm) REVERT: B 158 CYS cc_start: 0.9000 (m) cc_final: 0.8728 (m) REVERT: B 160 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8991 (mmtp) REVERT: B 169 MET cc_start: 0.9458 (tpp) cc_final: 0.9074 (mmm) REVERT: B 188 MET cc_start: 0.9673 (ttp) cc_final: 0.9216 (mmm) REVERT: B 252 MET cc_start: 0.9461 (ttp) cc_final: 0.9178 (ttm) REVERT: B 253 GLN cc_start: 0.9428 (pt0) cc_final: 0.9112 (pp30) REVERT: B 427 MET cc_start: 0.8953 (mtp) cc_final: 0.8637 (ptp) REVERT: B 441 CYS cc_start: 0.9146 (t) cc_final: 0.8786 (p) REVERT: B 464 MET cc_start: 0.9266 (ppp) cc_final: 0.8963 (ppp) REVERT: B 545 LEU cc_start: 0.9719 (tp) cc_final: 0.9510 (tp) REVERT: B 564 ASP cc_start: 0.9069 (m-30) cc_final: 0.8506 (t70) REVERT: B 568 PHE cc_start: 0.9236 (m-80) cc_final: 0.8976 (m-10) REVERT: B 569 MET cc_start: 0.9268 (ttm) cc_final: 0.8760 (mtp) REVERT: B 583 MET cc_start: 0.9622 (mmt) cc_final: 0.9189 (mmm) REVERT: B 650 LEU cc_start: 0.9660 (mm) cc_final: 0.9283 (tt) REVERT: B 654 LEU cc_start: 0.9842 (mp) cc_final: 0.9626 (mp) REVERT: B 657 MET cc_start: 0.9123 (mmp) cc_final: 0.8747 (tmm) REVERT: B 658 ILE cc_start: 0.9639 (mt) cc_final: 0.9268 (mt) REVERT: B 668 ASP cc_start: 0.8731 (m-30) cc_final: 0.8348 (m-30) REVERT: B 672 GLU cc_start: 0.9745 (mt-10) cc_final: 0.9430 (mm-30) REVERT: C 61 MET cc_start: 0.9533 (mmp) cc_final: 0.9300 (mmm) REVERT: C 158 CYS cc_start: 0.8998 (m) cc_final: 0.8724 (m) REVERT: C 160 LYS cc_start: 0.9328 (mmtt) cc_final: 0.8993 (mmtp) REVERT: C 169 MET cc_start: 0.9459 (tpp) cc_final: 0.9075 (mmm) REVERT: C 188 MET cc_start: 0.9672 (ttp) cc_final: 0.9215 (mmm) REVERT: C 252 MET cc_start: 0.9461 (ttp) cc_final: 0.9178 (ttm) REVERT: C 253 GLN cc_start: 0.9428 (pt0) cc_final: 0.9110 (pp30) REVERT: C 427 MET cc_start: 0.8953 (mtp) cc_final: 0.8637 (ptp) REVERT: C 441 CYS cc_start: 0.9145 (t) cc_final: 0.8785 (p) REVERT: C 464 MET cc_start: 0.9268 (ppp) cc_final: 0.8964 (ppp) REVERT: C 545 LEU cc_start: 0.9719 (tp) cc_final: 0.9511 (tp) REVERT: C 564 ASP cc_start: 0.9068 (m-30) cc_final: 0.8512 (t70) REVERT: C 568 PHE cc_start: 0.9234 (m-80) cc_final: 0.8972 (m-10) REVERT: C 569 MET cc_start: 0.9269 (ttm) cc_final: 0.8761 (mtp) REVERT: C 583 MET cc_start: 0.9622 (mmt) cc_final: 0.9191 (mmm) REVERT: C 650 LEU cc_start: 0.9660 (mm) cc_final: 0.9285 (tt) REVERT: C 654 LEU cc_start: 0.9843 (mp) cc_final: 0.9624 (mp) REVERT: C 657 MET cc_start: 0.9125 (mmp) cc_final: 0.8748 (tmm) REVERT: C 658 ILE cc_start: 0.9639 (mt) cc_final: 0.9261 (mt) REVERT: C 668 ASP cc_start: 0.8731 (m-30) cc_final: 0.8348 (m-30) REVERT: C 672 GLU cc_start: 0.9746 (mt-10) cc_final: 0.9430 (mm-30) REVERT: D 61 MET cc_start: 0.9533 (mmp) cc_final: 0.9300 (mmm) REVERT: D 158 CYS cc_start: 0.9015 (m) cc_final: 0.8580 (m) REVERT: D 160 LYS cc_start: 0.9342 (mmtt) cc_final: 0.8804 (mmtp) REVERT: D 188 MET cc_start: 0.9672 (ttp) cc_final: 0.9215 (mmm) REVERT: D 252 MET cc_start: 0.9462 (ttp) cc_final: 0.9177 (ttm) REVERT: D 427 MET cc_start: 0.8953 (mtp) cc_final: 0.8637 (ptp) REVERT: D 441 CYS cc_start: 0.9147 (t) cc_final: 0.8787 (p) REVERT: D 464 MET cc_start: 0.9267 (ppp) cc_final: 0.8963 (ppp) REVERT: D 545 LEU cc_start: 0.9717 (tp) cc_final: 0.9508 (tp) REVERT: D 564 ASP cc_start: 0.9030 (m-30) cc_final: 0.8433 (t70) REVERT: D 568 PHE cc_start: 0.9243 (m-80) cc_final: 0.9004 (m-10) REVERT: D 569 MET cc_start: 0.9269 (ttm) cc_final: 0.8759 (mtp) REVERT: D 583 MET cc_start: 0.9622 (mmt) cc_final: 0.9190 (mmm) REVERT: D 650 LEU cc_start: 0.9657 (mm) cc_final: 0.9285 (tt) REVERT: D 657 MET cc_start: 0.9155 (mmp) cc_final: 0.8745 (tmm) REVERT: D 668 ASP cc_start: 0.8728 (m-30) cc_final: 0.8345 (m-30) REVERT: D 672 GLU cc_start: 0.9756 (mt-10) cc_final: 0.9421 (mm-30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2779 time to fit residues: 162.2678 Evaluate side-chains 261 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 221 optimal weight: 0.8980 chunk 179 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 65 optimal weight: 30.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4860 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: