Starting phenix.real_space_refine on Tue Apr 9 01:26:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2024/6lba_0868.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2024/6lba_0868.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/6lba_0868/04_2024/6lba_0868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2024/6lba_0868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2024/6lba_0868.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2024/6lba_0868.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 100 5.16 5 C 9656 2.51 5 N 2624 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C ASP 530": "OD1" <-> "OD2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 518": "OD1" <-> "OD2" Residue "D ASP 530": "OD1" <-> "OD2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3748 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 12 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3748 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 12 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3748 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 12 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3748 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 12 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 8.20, per 1000 atoms: 0.55 Number of scatterers: 14992 At special positions: 0 Unit cell: (108.443, 126.734, 103.217, 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 100 16.00 O 2612 8.00 N 2624 7.00 C 9656 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: 6.15 Conformation dependent library (CDL) restraints added in 2.7 seconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3592 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 64.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid -1 through 19 Processing helix chain 'A' and resid 30 through 53 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 88 Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.690A pdb=" N SER A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.912A pdb=" N ALA A 126 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 170 through 171 No H-bonds generated for 'chain 'A' and resid 170 through 171' Processing helix chain 'A' and resid 173 through 174 No H-bonds generated for 'chain 'A' and resid 173 through 174' Processing helix chain 'A' and resid 175 through 198 removed outlier: 3.688A pdb=" N HIS A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG A 185 " --> pdb=" O TRP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.609A pdb=" N SER A 280 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.520A pdb=" N TYR A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS A 351 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.698A pdb=" N TRP A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 432 through 447 removed outlier: 4.064A pdb=" N SER A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 478 through 490 removed outlier: 3.656A pdb=" N VAL A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 484 " --> pdb=" O THR A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 541 removed outlier: 4.192A pdb=" N LEU A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.609A pdb=" N TYR A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 0 through 19 Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 65 through 88 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 104 through 118 removed outlier: 3.690A pdb=" N SER C 118 " --> pdb=" O PHE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.912A pdb=" N ALA C 126 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU C 139 " --> pdb=" O PRO C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 170 through 171 No H-bonds generated for 'chain 'C' and resid 170 through 171' Processing helix chain 'C' and resid 173 through 174 No H-bonds generated for 'chain 'C' and resid 173 through 174' Processing helix chain 'C' and resid 175 through 198 removed outlier: 3.687A pdb=" N HIS C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG C 185 " --> pdb=" O TRP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.610A pdb=" N SER C 280 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 281 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 removed outlier: 3.519A pdb=" N TYR C 318 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR C 349 " --> pdb=" O ARG C 345 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS C 351 " --> pdb=" O MET C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.698A pdb=" N TRP C 406 " --> pdb=" O PRO C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 432 through 447 removed outlier: 4.064A pdb=" N SER C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 478 through 490 removed outlier: 3.657A pdb=" N VAL C 482 " --> pdb=" O PRO C 478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 484 " --> pdb=" O THR C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG C 504 " --> pdb=" O SER C 500 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 541 removed outlier: 4.193A pdb=" N LEU C 534 " --> pdb=" O ASP C 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 555 through 570 removed outlier: 3.609A pdb=" N TYR C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 0 through 19 Processing helix chain 'B' and resid 30 through 53 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.690A pdb=" N SER B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.911A pdb=" N ALA B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 170 through 171 No H-bonds generated for 'chain 'B' and resid 170 through 171' Processing helix chain 'B' and resid 173 through 174 No H-bonds generated for 'chain 'B' and resid 173 through 174' Processing helix chain 'B' and resid 175 through 198 removed outlier: 3.688A pdb=" N HIS B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG B 185 " --> pdb=" O TRP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 275 through 284 removed outlier: 3.609A pdb=" N SER B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 320 removed outlier: 3.519A pdb=" N TYR B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 351 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.698A pdb=" N TRP B 406 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 432 through 447 removed outlier: 4.063A pdb=" N SER B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.657A pdb=" N VAL B 482 " --> pdb=" O PRO B 478 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 484 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 541 removed outlier: 4.192A pdb=" N LEU B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.609A pdb=" N TYR B 563 " --> pdb=" O GLN B 559 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 0 through 19 Processing helix chain 'D' and resid 30 through 53 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 65 through 88 Processing helix chain 'D' and resid 91 through 99 Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.689A pdb=" N SER D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.912A pdb=" N ALA D 126 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU D 139 " --> pdb=" O PRO D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 170 through 171 No H-bonds generated for 'chain 'D' and resid 170 through 171' Processing helix chain 'D' and resid 173 through 174 No H-bonds generated for 'chain 'D' and resid 173 through 174' Processing helix chain 'D' and resid 175 through 198 removed outlier: 3.687A pdb=" N HIS D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG D 185 " --> pdb=" O TRP D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.610A pdb=" N SER D 280 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 320 removed outlier: 3.521A pdb=" N TYR D 318 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 320 " --> pdb=" O GLN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS D 351 " --> pdb=" O MET D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 3.697A pdb=" N TRP D 406 " --> pdb=" O PRO D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 Processing helix chain 'D' and resid 432 through 447 removed outlier: 4.064A pdb=" N SER D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 478 through 490 removed outlier: 3.656A pdb=" N VAL D 482 " --> pdb=" O PRO D 478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 484 " --> pdb=" O THR D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG D 504 " --> pdb=" O SER D 500 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 541 removed outlier: 4.192A pdb=" N LEU D 534 " --> pdb=" O ASP D 530 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 554 No H-bonds generated for 'chain 'D' and resid 552 through 554' Processing helix chain 'D' and resid 555 through 570 removed outlier: 3.608A pdb=" N TYR D 563 " --> pdb=" O GLN D 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA2, first strand: chain 'C' and resid 365 through 366 Processing sheet with id=AA3, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'D' and resid 365 through 366 737 hydrogen bonds defined for protein. 2091 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: 4.41 Time building geometry restraints manager: 6.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4816 1.34 - 1.46: 3305 1.46 - 1.58: 7047 1.58 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 15320 Sorted by residual: bond pdb=" N PRO A 403 " pdb=" CD PRO A 403 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N PRO B 403 " pdb=" CD PRO B 403 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" N PRO C 403 " pdb=" CD PRO C 403 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.46e+01 bond pdb=" N PHE C 331 " pdb=" CA PHE C 331 " ideal model delta sigma weight residual 1.458 1.425 0.032 1.22e-02 6.72e+03 7.02e+00 ... (remaining 15315 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.97: 376 105.97 - 112.99: 8249 112.99 - 120.00: 5276 120.00 - 127.01: 6515 127.01 - 134.02: 224 Bond angle restraints: 20640 Sorted by residual: angle pdb=" CA PRO B 403 " pdb=" N PRO B 403 " pdb=" CD PRO B 403 " ideal model delta sigma weight residual 112.00 98.96 13.04 1.40e+00 5.10e-01 8.67e+01 angle pdb=" CA PRO C 403 " pdb=" N PRO C 403 " pdb=" CD PRO C 403 " ideal model delta sigma weight residual 112.00 98.97 13.03 1.40e+00 5.10e-01 8.67e+01 angle pdb=" CA PRO A 403 " pdb=" N PRO A 403 " pdb=" CD PRO A 403 " ideal model delta sigma weight residual 112.00 98.98 13.02 1.40e+00 5.10e-01 8.64e+01 angle pdb=" N ARG B 540 " pdb=" CA ARG B 540 " pdb=" C ARG B 540 " ideal model delta sigma weight residual 111.07 121.01 -9.94 1.07e+00 8.73e-01 8.64e+01 angle pdb=" CA PRO D 403 " pdb=" N PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 112.00 99.00 13.00 1.40e+00 5.10e-01 8.62e+01 ... (remaining 20635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 8056 16.04 - 32.08: 884 32.08 - 48.12: 228 48.12 - 64.16: 32 64.16 - 80.20: 12 Dihedral angle restraints: 9212 sinusoidal: 3760 harmonic: 5452 Sorted by residual: dihedral pdb=" CA HIS C 100 " pdb=" C HIS C 100 " pdb=" N GLN C 101 " pdb=" CA GLN C 101 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.36e+01 dihedral pdb=" CA HIS D 100 " pdb=" C HIS D 100 " pdb=" N GLN D 101 " pdb=" CA GLN D 101 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.35e+01 dihedral pdb=" CA HIS A 100 " pdb=" C HIS A 100 " pdb=" N GLN A 101 " pdb=" CA GLN A 101 " ideal model delta harmonic sigma weight residual 180.00 134.32 45.68 0 5.00e+00 4.00e-02 8.35e+01 ... (remaining 9209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1944 0.077 - 0.154: 254 0.154 - 0.230: 51 0.230 - 0.307: 11 0.307 - 0.384: 8 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA THR D 206 " pdb=" N THR D 206 " pdb=" C THR D 206 " pdb=" CB THR D 206 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA THR A 206 " pdb=" N THR A 206 " pdb=" C THR A 206 " pdb=" CB THR A 206 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA THR B 206 " pdb=" N THR B 206 " pdb=" C THR B 206 " pdb=" CB THR B 206 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 2265 not shown) Planarity restraints: 2596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 333 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO D 334 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO D 334 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 334 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 333 " -0.082 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO A 334 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 333 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO C 334 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO C 334 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 334 " 0.073 5.00e-02 4.00e+02 ... (remaining 2593 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 93 2.26 - 2.92: 7786 2.92 - 3.58: 22983 3.58 - 4.24: 33090 4.24 - 4.90: 53716 Nonbonded interactions: 117668 Sorted by model distance: nonbonded pdb=" O LEU C 539 " pdb=" CG PRO C 543 " model vdw 1.605 3.440 nonbonded pdb=" O LEU D 539 " pdb=" CG PRO D 543 " model vdw 1.605 3.440 nonbonded pdb=" O LEU A 539 " pdb=" CG PRO A 543 " model vdw 1.606 3.440 nonbonded pdb=" O LEU B 539 " pdb=" CG PRO B 543 " model vdw 1.606 3.440 nonbonded pdb=" O LEU D 360 " pdb=" OD1 ASN D 361 " model vdw 1.858 3.040 ... (remaining 117663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.370 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 41.270 Find NCS groups from input model: 0.960 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 0.054 15320 Z= 0.350 Angle : 1.039 13.037 20640 Z= 0.716 Chirality : 0.062 0.384 2268 Planarity : 0.007 0.125 2596 Dihedral : 14.227 80.205 5620 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 70.19 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.91 % Favored : 88.64 % Rotamer: Outliers : 3.56 % Allowed : 6.87 % Favored : 89.57 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.46 (0.19), residues: 1760 helix: -1.28 (0.15), residues: 1060 sheet: -1.66 (0.75), residues: 56 loop : -2.03 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 186 HIS 0.005 0.001 HIS C 357 PHE 0.011 0.001 PHE B 117 TYR 0.011 0.002 TYR C 82 ARG 0.002 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 455 time to evaluate : 1.863 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: A 2 GLU cc_start: 0.8234 (tp30) cc_final: 0.7809 (tp30) REVERT: A 28 GLN cc_start: 0.7879 (pt0) cc_final: 0.7652 (pp30) REVERT: A 31 CYS cc_start: 0.8266 (p) cc_final: 0.7496 (p) REVERT: A 54 LYS cc_start: 0.8453 (mttt) cc_final: 0.8008 (mttp) REVERT: A 84 LYS cc_start: 0.9394 (mtpt) cc_final: 0.8785 (ttpt) REVERT: A 148 LYS cc_start: 0.8677 (tttt) cc_final: 0.8454 (ttpp) REVERT: A 171 ARG cc_start: 0.7339 (mtt180) cc_final: 0.7011 (mtt90) REVERT: A 178 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 186 TRP cc_start: 0.6976 (m-90) cc_final: 0.6742 (m-10) REVERT: A 190 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7124 (tm-30) REVERT: A 430 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.6337 (p-80) REVERT: A 439 MET cc_start: 0.7960 (mmm) cc_final: 0.7613 (mmm) REVERT: A 487 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6769 (mmm160) REVERT: A 514 VAL cc_start: 0.9180 (t) cc_final: 0.8875 (m) REVERT: A 534 LEU cc_start: 0.7152 (mt) cc_final: 0.6893 (mt) REVERT: C 1 MET cc_start: 0.9036 (tpt) cc_final: 0.8825 (tpt) REVERT: C 2 GLU cc_start: 0.8310 (tp30) cc_final: 0.7937 (tp30) REVERT: C 31 CYS cc_start: 0.8293 (p) cc_final: 0.7511 (p) REVERT: C 54 LYS cc_start: 0.8542 (mttt) cc_final: 0.8129 (mttp) REVERT: C 84 LYS cc_start: 0.9357 (mtpt) cc_final: 0.8729 (ttpt) REVERT: C 148 LYS cc_start: 0.8795 (tttt) cc_final: 0.8578 (ttpp) REVERT: C 171 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7129 (mtt90) REVERT: C 178 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7742 (tm-30) REVERT: C 186 TRP cc_start: 0.6928 (m-90) cc_final: 0.6572 (m-10) REVERT: C 190 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7187 (tm-30) REVERT: C 439 MET cc_start: 0.7958 (mmm) cc_final: 0.7401 (mmm) REVERT: C 487 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6844 (mmm160) REVERT: C 514 VAL cc_start: 0.9230 (t) cc_final: 0.8961 (m) REVERT: B 1 MET cc_start: 0.8969 (tpt) cc_final: 0.8767 (tpt) REVERT: B 2 GLU cc_start: 0.8295 (tp30) cc_final: 0.7934 (tp30) REVERT: B 54 LYS cc_start: 0.8606 (mttt) cc_final: 0.8177 (mttp) REVERT: B 171 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7209 (mtt90) REVERT: B 178 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 212 ASP cc_start: 0.9156 (m-30) cc_final: 0.8952 (m-30) REVERT: B 345 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7748 (tpm170) REVERT: B 439 MET cc_start: 0.7919 (mmm) cc_final: 0.7405 (mmm) REVERT: B 514 VAL cc_start: 0.9281 (t) cc_final: 0.9002 (m) REVERT: D 2 GLU cc_start: 0.8231 (tp30) cc_final: 0.7833 (tp30) REVERT: D 24 ILE cc_start: 0.7826 (mm) cc_final: 0.7623 (mt) REVERT: D 28 GLN cc_start: 0.7931 (pt0) cc_final: 0.7723 (pp30) REVERT: D 31 CYS cc_start: 0.8435 (p) cc_final: 0.7629 (p) REVERT: D 54 LYS cc_start: 0.8487 (mttt) cc_final: 0.8017 (mttp) REVERT: D 84 LYS cc_start: 0.9313 (mtpt) cc_final: 0.8721 (ttpt) REVERT: D 171 ARG cc_start: 0.7369 (mtt180) cc_final: 0.6960 (mtt90) REVERT: D 178 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7641 (tm-30) REVERT: D 190 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7236 (tm-30) REVERT: D 439 MET cc_start: 0.7950 (mmm) cc_final: 0.7364 (mmm) REVERT: D 487 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6847 (mmm160) REVERT: D 514 VAL cc_start: 0.9147 (t) cc_final: 0.8874 (m) outliers start: 56 outliers final: 25 residues processed: 479 average time/residue: 0.3276 time to fit residues: 215.9337 Evaluate side-chains 375 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 345 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 167 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS A 312 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN C 109 HIS C 312 HIS ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 109 HIS B 312 HIS ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 51 GLN D 109 HIS D 312 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15320 Z= 0.242 Angle : 0.692 5.998 20640 Z= 0.363 Chirality : 0.043 0.189 2268 Planarity : 0.005 0.054 2596 Dihedral : 5.928 41.026 1976 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.97 (0.20), residues: 1760 helix: 0.17 (0.15), residues: 1092 sheet: -1.00 (0.80), residues: 56 loop : -2.02 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 489 HIS 0.005 0.001 HIS B 366 PHE 0.019 0.002 PHE B 377 TYR 0.020 0.002 TYR A 376 ARG 0.005 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 1.909 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: A 31 CYS cc_start: 0.8011 (p) cc_final: 0.7267 (p) REVERT: A 49 ILE cc_start: 0.9474 (mt) cc_final: 0.9267 (mm) REVERT: A 54 LYS cc_start: 0.8434 (mttt) cc_final: 0.7999 (mttp) REVERT: A 84 LYS cc_start: 0.9335 (mtpt) cc_final: 0.8677 (ttpt) REVERT: A 148 LYS cc_start: 0.8713 (tttt) cc_final: 0.8313 (ttpt) REVERT: A 149 TYR cc_start: 0.8451 (m-10) cc_final: 0.8054 (m-10) REVERT: A 190 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7256 (tm-30) REVERT: A 311 MET cc_start: 0.8150 (pmm) cc_final: 0.7623 (pmm) REVERT: A 340 MET cc_start: 0.8104 (mtm) cc_final: 0.7789 (mtt) REVERT: A 366 HIS cc_start: 0.6342 (m-70) cc_final: 0.5927 (m170) REVERT: A 487 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7496 (mmm160) REVERT: C 2 GLU cc_start: 0.7870 (tp30) cc_final: 0.7298 (tp30) REVERT: C 31 CYS cc_start: 0.8100 (p) cc_final: 0.7292 (p) REVERT: C 49 ILE cc_start: 0.9503 (mt) cc_final: 0.9234 (mm) REVERT: C 54 LYS cc_start: 0.8452 (mttt) cc_final: 0.7983 (mttp) REVERT: C 84 LYS cc_start: 0.9326 (mtpt) cc_final: 0.8715 (ttpt) REVERT: C 148 LYS cc_start: 0.8772 (tttt) cc_final: 0.8253 (ttpt) REVERT: C 155 ASP cc_start: 0.7694 (t70) cc_final: 0.7482 (m-30) REVERT: C 186 TRP cc_start: 0.6754 (m-10) cc_final: 0.6486 (m-10) REVERT: C 190 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7220 (tm-30) REVERT: C 311 MET cc_start: 0.8247 (pmm) cc_final: 0.7675 (pmm) REVERT: C 366 HIS cc_start: 0.6512 (m-70) cc_final: 0.6308 (m170) REVERT: C 487 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7813 (mmm160) REVERT: B 2 GLU cc_start: 0.7869 (tp30) cc_final: 0.7262 (tp30) REVERT: B 49 ILE cc_start: 0.9514 (mt) cc_final: 0.9279 (mm) REVERT: B 54 LYS cc_start: 0.8508 (mttt) cc_final: 0.8034 (mttp) REVERT: B 84 LYS cc_start: 0.9273 (mtpt) cc_final: 0.8695 (ttpt) REVERT: B 89 ASN cc_start: 0.8345 (p0) cc_final: 0.8045 (p0) REVERT: B 148 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8468 (ttpt) REVERT: B 311 MET cc_start: 0.8300 (pmm) cc_final: 0.7316 (ptp) REVERT: B 340 MET cc_start: 0.8260 (mtm) cc_final: 0.7975 (mtt) REVERT: B 366 HIS cc_start: 0.6073 (m-70) cc_final: 0.3983 (m-70) REVERT: D 2 GLU cc_start: 0.7832 (tp30) cc_final: 0.7215 (tp30) REVERT: D 28 GLN cc_start: 0.7839 (pt0) cc_final: 0.7624 (pp30) REVERT: D 54 LYS cc_start: 0.8410 (mttt) cc_final: 0.7847 (mttp) REVERT: D 84 LYS cc_start: 0.9337 (mtpt) cc_final: 0.8721 (ttpt) REVERT: D 148 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8436 (tttm) REVERT: D 149 TYR cc_start: 0.8507 (m-10) cc_final: 0.8064 (m-10) REVERT: D 155 ASP cc_start: 0.7697 (t70) cc_final: 0.6896 (t0) REVERT: D 171 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6984 (mtt90) REVERT: D 190 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7287 (tm-30) REVERT: D 311 MET cc_start: 0.8193 (pmm) cc_final: 0.7542 (pmm) REVERT: D 340 MET cc_start: 0.8312 (mtm) cc_final: 0.8083 (mtt) REVERT: D 366 HIS cc_start: 0.6255 (m-70) cc_final: 0.5888 (m170) REVERT: D 487 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7539 (mmm160) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.3112 time to fit residues: 215.3317 Evaluate side-chains 360 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 ASN A 102 ASN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 102 ASN ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15320 Z= 0.244 Angle : 0.648 5.709 20640 Z= 0.342 Chirality : 0.042 0.145 2268 Planarity : 0.004 0.028 2596 Dihedral : 5.776 39.272 1976 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.25 (0.21), residues: 1760 helix: 0.79 (0.16), residues: 1076 sheet: -0.99 (0.78), residues: 56 loop : -1.77 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 186 HIS 0.006 0.001 HIS A 366 PHE 0.034 0.002 PHE A 442 TYR 0.026 0.002 TYR B 435 ARG 0.009 0.001 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 time to evaluate : 1.715 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: A 1 MET cc_start: 0.8841 (tpt) cc_final: 0.8635 (tpt) REVERT: A 31 CYS cc_start: 0.8275 (p) cc_final: 0.7582 (p) REVERT: A 49 ILE cc_start: 0.9518 (mt) cc_final: 0.9309 (mm) REVERT: A 54 LYS cc_start: 0.8509 (mttt) cc_final: 0.7971 (mttp) REVERT: A 84 LYS cc_start: 0.9369 (mtpt) cc_final: 0.8746 (ttpt) REVERT: A 92 TRP cc_start: 0.8738 (t60) cc_final: 0.8210 (t60) REVERT: A 148 LYS cc_start: 0.8688 (tttt) cc_final: 0.8273 (ttpt) REVERT: A 149 TYR cc_start: 0.8368 (m-10) cc_final: 0.7999 (m-10) REVERT: A 155 ASP cc_start: 0.7156 (t0) cc_final: 0.6798 (m-30) REVERT: A 184 ASP cc_start: 0.8363 (p0) cc_final: 0.8157 (p0) REVERT: A 185 ARG cc_start: 0.8447 (mtp180) cc_final: 0.8242 (ttt-90) REVERT: A 186 TRP cc_start: 0.6911 (m-10) cc_final: 0.6646 (m-10) REVERT: A 190 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7390 (tm-30) REVERT: A 347 MET cc_start: 0.8478 (tpp) cc_final: 0.8189 (tpt) REVERT: A 435 TYR cc_start: 0.7804 (t80) cc_final: 0.7372 (t80) REVERT: A 442 PHE cc_start: 0.6131 (m-80) cc_final: 0.5491 (m-80) REVERT: C 2 GLU cc_start: 0.8013 (tp30) cc_final: 0.7374 (tp30) REVERT: C 31 CYS cc_start: 0.8344 (p) cc_final: 0.7555 (p) REVERT: C 37 LEU cc_start: 0.9669 (mt) cc_final: 0.9321 (tp) REVERT: C 49 ILE cc_start: 0.9589 (mt) cc_final: 0.9381 (mm) REVERT: C 54 LYS cc_start: 0.8512 (mttt) cc_final: 0.8014 (mttp) REVERT: C 84 LYS cc_start: 0.9370 (mtpt) cc_final: 0.8782 (ttpt) REVERT: C 92 TRP cc_start: 0.8741 (t60) cc_final: 0.8111 (t60) REVERT: C 148 LYS cc_start: 0.8658 (tttt) cc_final: 0.8130 (ttpt) REVERT: C 190 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7291 (tm-30) REVERT: C 340 MET cc_start: 0.8525 (mtt) cc_final: 0.8319 (mtt) REVERT: C 435 TYR cc_start: 0.7876 (t80) cc_final: 0.6828 (t80) REVERT: C 461 MET cc_start: 0.5371 (mpp) cc_final: 0.4513 (mmp) REVERT: C 487 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7754 (mmm160) REVERT: C 494 SER cc_start: 0.8835 (m) cc_final: 0.8558 (t) REVERT: B 2 GLU cc_start: 0.7942 (tp30) cc_final: 0.7353 (tp30) REVERT: B 31 CYS cc_start: 0.8290 (p) cc_final: 0.7695 (p) REVERT: B 48 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 49 ILE cc_start: 0.9529 (mt) cc_final: 0.9319 (mm) REVERT: B 54 LYS cc_start: 0.8424 (mttt) cc_final: 0.7928 (mttp) REVERT: B 84 LYS cc_start: 0.9344 (mtpt) cc_final: 0.8735 (ttpt) REVERT: B 89 ASN cc_start: 0.8257 (p0) cc_final: 0.7989 (p0) REVERT: B 92 TRP cc_start: 0.8873 (t60) cc_final: 0.8532 (t60) REVERT: B 148 LYS cc_start: 0.8760 (ttpp) cc_final: 0.8458 (ttpt) REVERT: B 435 TYR cc_start: 0.7845 (t80) cc_final: 0.7364 (t80) REVERT: B 461 MET cc_start: 0.4763 (mpp) cc_final: 0.4121 (mmp) REVERT: D 2 GLU cc_start: 0.7905 (tp30) cc_final: 0.7363 (tp30) REVERT: D 28 GLN cc_start: 0.8082 (pt0) cc_final: 0.7640 (pp30) REVERT: D 31 CYS cc_start: 0.8378 (p) cc_final: 0.7712 (p) REVERT: D 37 LEU cc_start: 0.9631 (mt) cc_final: 0.9284 (tp) REVERT: D 54 LYS cc_start: 0.8446 (mttt) cc_final: 0.7925 (mttp) REVERT: D 84 LYS cc_start: 0.9334 (mtpt) cc_final: 0.8881 (ttmt) REVERT: D 149 TYR cc_start: 0.8427 (m-10) cc_final: 0.8032 (m-10) REVERT: D 155 ASP cc_start: 0.7032 (t70) cc_final: 0.6616 (m-30) REVERT: D 158 MET cc_start: 0.8452 (tmm) cc_final: 0.8221 (tmm) REVERT: D 190 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7351 (tm-30) REVERT: D 347 MET cc_start: 0.8545 (tpp) cc_final: 0.8327 (tpp) REVERT: D 435 TYR cc_start: 0.7890 (t80) cc_final: 0.7501 (t80) REVERT: D 494 SER cc_start: 0.8873 (m) cc_final: 0.8570 (t) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.2749 time to fit residues: 180.8615 Evaluate side-chains 349 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS A 111 HIS A 187 ASN ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 59 HIS C 187 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS B 111 HIS B 187 ASN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 111 HIS ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15320 Z= 0.198 Angle : 0.649 10.807 20640 Z= 0.336 Chirality : 0.040 0.130 2268 Planarity : 0.004 0.028 2596 Dihedral : 5.678 37.531 1976 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.15 (0.21), residues: 1760 helix: 1.08 (0.17), residues: 1076 sheet: -0.70 (0.77), residues: 56 loop : -1.57 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 186 HIS 0.010 0.001 HIS B 490 PHE 0.030 0.002 PHE B 442 TYR 0.016 0.001 TYR B 116 ARG 0.008 0.001 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 1.665 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 28 GLN cc_start: 0.8147 (pt0) cc_final: 0.7476 (pp30) REVERT: A 54 LYS cc_start: 0.8569 (mttt) cc_final: 0.8010 (mttp) REVERT: A 84 LYS cc_start: 0.9368 (mtpt) cc_final: 0.8921 (ttmt) REVERT: A 92 TRP cc_start: 0.8756 (t60) cc_final: 0.8246 (t60) REVERT: A 138 MET cc_start: 0.7623 (ptt) cc_final: 0.7422 (mmt) REVERT: A 148 LYS cc_start: 0.8725 (tttt) cc_final: 0.8392 (ttpt) REVERT: A 149 TYR cc_start: 0.8383 (m-10) cc_final: 0.8053 (m-10) REVERT: A 155 ASP cc_start: 0.7255 (t0) cc_final: 0.6767 (m-30) REVERT: A 158 MET cc_start: 0.8218 (tmm) cc_final: 0.7903 (tmm) REVERT: A 185 ARG cc_start: 0.8566 (mtp180) cc_final: 0.8330 (ttt-90) REVERT: A 186 TRP cc_start: 0.6949 (m-10) cc_final: 0.6656 (m-10) REVERT: A 190 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7302 (tm-30) REVERT: A 461 MET cc_start: 0.4376 (mpp) cc_final: 0.3771 (mmp) REVERT: A 487 ARG cc_start: 0.8121 (mmt90) cc_final: 0.7772 (mmm160) REVERT: C 2 GLU cc_start: 0.7929 (tp30) cc_final: 0.7384 (tp30) REVERT: C 28 GLN cc_start: 0.8108 (pt0) cc_final: 0.7476 (pp30) REVERT: C 31 CYS cc_start: 0.8412 (p) cc_final: 0.8032 (p) REVERT: C 37 LEU cc_start: 0.9684 (mt) cc_final: 0.9315 (tp) REVERT: C 49 ILE cc_start: 0.9534 (mt) cc_final: 0.9325 (mm) REVERT: C 54 LYS cc_start: 0.8376 (mttt) cc_final: 0.7867 (mttp) REVERT: C 84 LYS cc_start: 0.9382 (mtpt) cc_final: 0.8931 (ttmt) REVERT: C 92 TRP cc_start: 0.8688 (t60) cc_final: 0.8257 (t60) REVERT: C 190 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7331 (tm-30) REVERT: C 340 MET cc_start: 0.8317 (mtt) cc_final: 0.7934 (mtt) REVERT: C 431 LYS cc_start: 0.9025 (mttt) cc_final: 0.8392 (mmmt) REVERT: C 435 TYR cc_start: 0.8406 (t80) cc_final: 0.8128 (t80) REVERT: C 461 MET cc_start: 0.4812 (mpp) cc_final: 0.4166 (mmp) REVERT: C 473 PHE cc_start: 0.7076 (m-80) cc_final: 0.6477 (m-10) REVERT: C 567 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 2 GLU cc_start: 0.7832 (tp30) cc_final: 0.7345 (tp30) REVERT: B 28 GLN cc_start: 0.8175 (pt0) cc_final: 0.7573 (pp30) REVERT: B 48 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8295 (mm-30) REVERT: B 54 LYS cc_start: 0.8352 (mttt) cc_final: 0.7747 (mttp) REVERT: B 84 LYS cc_start: 0.9366 (mtpt) cc_final: 0.8962 (ttpt) REVERT: B 89 ASN cc_start: 0.8311 (p0) cc_final: 0.8082 (p0) REVERT: B 92 TRP cc_start: 0.8913 (t60) cc_final: 0.8625 (t60) REVERT: B 148 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8412 (ttpt) REVERT: B 184 ASP cc_start: 0.8270 (p0) cc_final: 0.7991 (p0) REVERT: B 461 MET cc_start: 0.4907 (mpp) cc_final: 0.4147 (mmp) REVERT: D 2 GLU cc_start: 0.7794 (tp30) cc_final: 0.7297 (tp30) REVERT: D 24 ILE cc_start: 0.7917 (mm) cc_final: 0.7601 (mt) REVERT: D 28 GLN cc_start: 0.8107 (pt0) cc_final: 0.7586 (pp30) REVERT: D 31 CYS cc_start: 0.8363 (p) cc_final: 0.7894 (p) REVERT: D 37 LEU cc_start: 0.9606 (mt) cc_final: 0.9260 (tp) REVERT: D 54 LYS cc_start: 0.8439 (mttt) cc_final: 0.7789 (mttp) REVERT: D 84 LYS cc_start: 0.9345 (mtpt) cc_final: 0.8900 (ttmt) REVERT: D 148 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8019 (tmmt) REVERT: D 155 ASP cc_start: 0.6940 (t70) cc_final: 0.6505 (m-30) REVERT: D 158 MET cc_start: 0.8550 (tmm) cc_final: 0.8271 (tmm) REVERT: D 184 ASP cc_start: 0.8195 (p0) cc_final: 0.7929 (p0) REVERT: D 190 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7465 (tm-30) REVERT: D 347 MET cc_start: 0.8253 (tpp) cc_final: 0.8035 (tpp) REVERT: D 461 MET cc_start: 0.5031 (mpp) cc_final: 0.4352 (mmp) REVERT: D 487 ARG cc_start: 0.8049 (mmt90) cc_final: 0.7596 (mmm160) REVERT: D 515 VAL cc_start: 0.9210 (t) cc_final: 0.8974 (p) REVERT: D 539 LEU cc_start: 0.9214 (pp) cc_final: 0.8805 (mt) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.2800 time to fit residues: 175.6062 Evaluate side-chains 335 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 159 optimal weight: 0.0170 chunk 44 optimal weight: 3.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN B 187 ASN B 490 HIS ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15320 Z= 0.228 Angle : 0.632 7.439 20640 Z= 0.326 Chirality : 0.041 0.137 2268 Planarity : 0.004 0.047 2596 Dihedral : 5.537 36.583 1976 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.13 % Allowed : 2.23 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.18 (0.21), residues: 1760 helix: 0.95 (0.16), residues: 1116 sheet: -0.59 (0.78), residues: 56 loop : -1.36 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 186 HIS 0.005 0.001 HIS B 100 PHE 0.038 0.002 PHE A 442 TYR 0.025 0.001 TYR A 116 ARG 0.008 0.001 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 391 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8115 (pt0) cc_final: 0.7519 (pp30) REVERT: A 31 CYS cc_start: 0.8301 (p) cc_final: 0.7660 (p) REVERT: A 49 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9089 (mm) REVERT: A 54 LYS cc_start: 0.8481 (mttt) cc_final: 0.7819 (mttp) REVERT: A 84 LYS cc_start: 0.9376 (mtpt) cc_final: 0.9027 (ttpt) REVERT: A 92 TRP cc_start: 0.8748 (t60) cc_final: 0.8304 (t60) REVERT: A 155 ASP cc_start: 0.7205 (t0) cc_final: 0.6772 (m-30) REVERT: A 178 GLU cc_start: 0.8662 (mp0) cc_final: 0.8194 (mp0) REVERT: A 184 ASP cc_start: 0.8232 (p0) cc_final: 0.7942 (p0) REVERT: A 185 ARG cc_start: 0.8572 (mtp180) cc_final: 0.8285 (ttt-90) REVERT: A 186 TRP cc_start: 0.6920 (m-10) cc_final: 0.6711 (m-10) REVERT: A 190 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7409 (tm-30) REVERT: A 311 MET cc_start: 0.8345 (pmm) cc_final: 0.8122 (ptp) REVERT: A 347 MET cc_start: 0.8025 (tpp) cc_final: 0.7713 (tpp) REVERT: A 435 TYR cc_start: 0.7941 (t80) cc_final: 0.7461 (t80) REVERT: A 461 MET cc_start: 0.4753 (mpp) cc_final: 0.4080 (mmp) REVERT: A 487 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7820 (mmm160) REVERT: C 24 ILE cc_start: 0.7975 (mm) cc_final: 0.7743 (mt) REVERT: C 28 GLN cc_start: 0.8144 (pt0) cc_final: 0.7523 (pp30) REVERT: C 33 LEU cc_start: 0.9457 (tt) cc_final: 0.9089 (tp) REVERT: C 37 LEU cc_start: 0.9703 (mt) cc_final: 0.9348 (tp) REVERT: C 49 ILE cc_start: 0.9551 (mt) cc_final: 0.9332 (mm) REVERT: C 54 LYS cc_start: 0.8338 (mttt) cc_final: 0.7781 (mttp) REVERT: C 84 LYS cc_start: 0.9372 (mtpt) cc_final: 0.9003 (ttpt) REVERT: C 92 TRP cc_start: 0.8804 (t60) cc_final: 0.8178 (t60) REVERT: C 178 GLU cc_start: 0.8625 (mp0) cc_final: 0.8158 (mp0) REVERT: C 184 ASP cc_start: 0.8223 (p0) cc_final: 0.7950 (p0) REVERT: C 190 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7452 (tm-30) REVERT: C 311 MET cc_start: 0.8372 (pmm) cc_final: 0.8121 (ptp) REVERT: C 461 MET cc_start: 0.4887 (mpp) cc_final: 0.4286 (mmt) REVERT: C 487 ARG cc_start: 0.8183 (mmt90) cc_final: 0.7681 (mmm160) REVERT: B 2 GLU cc_start: 0.7924 (tp30) cc_final: 0.7479 (tp30) REVERT: B 24 ILE cc_start: 0.8047 (mm) cc_final: 0.7729 (mm) REVERT: B 28 GLN cc_start: 0.8354 (pt0) cc_final: 0.7552 (pp30) REVERT: B 31 CYS cc_start: 0.8239 (p) cc_final: 0.7549 (p) REVERT: B 48 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8443 (mm-30) REVERT: B 54 LYS cc_start: 0.8403 (mttt) cc_final: 0.7800 (mttp) REVERT: B 84 LYS cc_start: 0.9341 (mtpt) cc_final: 0.8985 (ttpt) REVERT: B 92 TRP cc_start: 0.8929 (t60) cc_final: 0.8651 (t60) REVERT: B 138 MET cc_start: 0.8388 (mmt) cc_final: 0.8097 (mmm) REVERT: B 311 MET cc_start: 0.8488 (pmm) cc_final: 0.8207 (ptp) REVERT: B 410 GLU cc_start: 0.8778 (pm20) cc_final: 0.8368 (pt0) REVERT: B 461 MET cc_start: 0.5074 (mpp) cc_final: 0.4552 (mmp) REVERT: B 567 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8150 (tm-30) REVERT: D 24 ILE cc_start: 0.8001 (mm) cc_final: 0.7796 (mt) REVERT: D 28 GLN cc_start: 0.8106 (pt0) cc_final: 0.7490 (pp30) REVERT: D 37 LEU cc_start: 0.9581 (mt) cc_final: 0.9287 (tp) REVERT: D 54 LYS cc_start: 0.8467 (mttt) cc_final: 0.7819 (mttp) REVERT: D 84 LYS cc_start: 0.9372 (mtpt) cc_final: 0.8910 (ttmt) REVERT: D 148 LYS cc_start: 0.8547 (ttpt) cc_final: 0.7961 (tmmt) REVERT: D 158 MET cc_start: 0.8508 (tmm) cc_final: 0.8194 (tmm) REVERT: D 178 GLU cc_start: 0.8661 (mp0) cc_final: 0.8159 (mp0) REVERT: D 184 ASP cc_start: 0.8274 (p0) cc_final: 0.8039 (p0) REVERT: D 190 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7476 (tm-30) REVERT: D 363 MET cc_start: 0.7559 (mtm) cc_final: 0.7345 (mtm) REVERT: D 461 MET cc_start: 0.4994 (mpp) cc_final: 0.4198 (mmp) REVERT: D 567 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8169 (tm-30) outliers start: 2 outliers final: 0 residues processed: 391 average time/residue: 0.2698 time to fit residues: 155.9670 Evaluate side-chains 321 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 320 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS B 490 HIS ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15320 Z= 0.247 Angle : 0.642 7.988 20640 Z= 0.331 Chirality : 0.041 0.137 2268 Planarity : 0.004 0.032 2596 Dihedral : 5.489 36.220 1976 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.18 (0.21), residues: 1760 helix: 0.90 (0.16), residues: 1120 sheet: -0.61 (0.76), residues: 56 loop : -1.26 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 186 HIS 0.006 0.001 HIS B 490 PHE 0.027 0.002 PHE A 442 TYR 0.022 0.001 TYR A 116 ARG 0.004 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.7981 (mm) cc_final: 0.7709 (mt) REVERT: A 28 GLN cc_start: 0.8277 (pt0) cc_final: 0.7583 (pp30) REVERT: A 31 CYS cc_start: 0.8410 (p) cc_final: 0.7952 (p) REVERT: A 49 ILE cc_start: 0.9319 (mp) cc_final: 0.9109 (mm) REVERT: A 54 LYS cc_start: 0.8640 (mttt) cc_final: 0.7835 (mttp) REVERT: A 84 LYS cc_start: 0.9388 (mtpt) cc_final: 0.8813 (ttpt) REVERT: A 138 MET cc_start: 0.8091 (mmt) cc_final: 0.7648 (ptt) REVERT: A 155 ASP cc_start: 0.7241 (t0) cc_final: 0.6672 (m-30) REVERT: A 165 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8421 (mptt) REVERT: A 178 GLU cc_start: 0.8629 (mp0) cc_final: 0.8176 (mp0) REVERT: A 184 ASP cc_start: 0.8175 (p0) cc_final: 0.7845 (p0) REVERT: A 185 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8306 (ttt-90) REVERT: A 190 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7343 (tm-30) REVERT: A 347 MET cc_start: 0.8184 (tpp) cc_final: 0.7590 (tpp) REVERT: A 442 PHE cc_start: 0.6799 (m-80) cc_final: 0.6527 (m-80) REVERT: A 461 MET cc_start: 0.5098 (mpp) cc_final: 0.4482 (mmp) REVERT: A 487 ARG cc_start: 0.8175 (mmt90) cc_final: 0.7932 (mmm160) REVERT: C 28 GLN cc_start: 0.8310 (pt0) cc_final: 0.7255 (pp30) REVERT: C 33 LEU cc_start: 0.9483 (tt) cc_final: 0.9126 (tp) REVERT: C 37 LEU cc_start: 0.9703 (mt) cc_final: 0.9365 (tp) REVERT: C 49 ILE cc_start: 0.9540 (mt) cc_final: 0.9319 (mm) REVERT: C 54 LYS cc_start: 0.8399 (mttt) cc_final: 0.7768 (mttp) REVERT: C 84 LYS cc_start: 0.9364 (mtpt) cc_final: 0.9024 (ttpt) REVERT: C 165 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8413 (mptt) REVERT: C 178 GLU cc_start: 0.8631 (mp0) cc_final: 0.8128 (mp0) REVERT: C 184 ASP cc_start: 0.8270 (p0) cc_final: 0.7997 (p0) REVERT: C 190 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7401 (tm-30) REVERT: C 461 MET cc_start: 0.5169 (mpp) cc_final: 0.4640 (mmt) REVERT: C 487 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7736 (mmm160) REVERT: B 24 ILE cc_start: 0.8226 (mm) cc_final: 0.7939 (mt) REVERT: B 28 GLN cc_start: 0.8415 (pt0) cc_final: 0.7475 (pp30) REVERT: B 48 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8396 (mm-30) REVERT: B 54 LYS cc_start: 0.8574 (mttt) cc_final: 0.7851 (mttp) REVERT: B 84 LYS cc_start: 0.9340 (mtpt) cc_final: 0.9010 (ttpt) REVERT: B 92 TRP cc_start: 0.8943 (t60) cc_final: 0.8655 (t60) REVERT: B 138 MET cc_start: 0.8412 (mmt) cc_final: 0.7953 (mmt) REVERT: B 165 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8450 (mptt) REVERT: B 184 ASP cc_start: 0.8263 (p0) cc_final: 0.7909 (p0) REVERT: B 347 MET cc_start: 0.8176 (tpp) cc_final: 0.7784 (tpp) REVERT: B 410 GLU cc_start: 0.8731 (pm20) cc_final: 0.8252 (tm-30) REVERT: B 461 MET cc_start: 0.5077 (mpp) cc_final: 0.4762 (mmp) REVERT: B 567 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8052 (tm-30) REVERT: D 24 ILE cc_start: 0.8098 (mm) cc_final: 0.7813 (mt) REVERT: D 28 GLN cc_start: 0.8178 (pt0) cc_final: 0.7571 (pp30) REVERT: D 31 CYS cc_start: 0.8461 (p) cc_final: 0.7991 (p) REVERT: D 54 LYS cc_start: 0.8491 (mttt) cc_final: 0.7847 (mttp) REVERT: D 84 LYS cc_start: 0.9371 (mtpt) cc_final: 0.8647 (ttmt) REVERT: D 158 MET cc_start: 0.8622 (tmm) cc_final: 0.8179 (tmm) REVERT: D 184 ASP cc_start: 0.8286 (p0) cc_final: 0.7957 (p0) REVERT: D 190 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7509 (tm-30) REVERT: D 461 MET cc_start: 0.5554 (mpp) cc_final: 0.4713 (mmp) REVERT: D 487 ARG cc_start: 0.8309 (mmt90) cc_final: 0.8003 (mmm160) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.2577 time to fit residues: 143.7054 Evaluate side-chains 317 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 0.0060 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 430 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS C 430 HIS ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15320 Z= 0.188 Angle : 0.618 9.334 20640 Z= 0.315 Chirality : 0.040 0.132 2268 Planarity : 0.004 0.035 2596 Dihedral : 5.359 35.682 1976 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.30 (0.21), residues: 1760 helix: 0.99 (0.16), residues: 1120 sheet: -0.54 (0.76), residues: 56 loop : -1.22 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 186 HIS 0.007 0.001 HIS A 430 PHE 0.024 0.001 PHE A 442 TYR 0.017 0.001 TYR A 116 ARG 0.004 0.000 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8304 (pt0) cc_final: 0.7590 (pp30) REVERT: A 54 LYS cc_start: 0.8600 (mttt) cc_final: 0.7942 (mttp) REVERT: A 84 LYS cc_start: 0.9372 (mtpt) cc_final: 0.8918 (ttmt) REVERT: A 155 ASP cc_start: 0.7053 (t0) cc_final: 0.6572 (m-30) REVERT: A 158 MET cc_start: 0.7855 (tmm) cc_final: 0.7501 (tmm) REVERT: A 178 GLU cc_start: 0.8653 (mp0) cc_final: 0.8222 (mp0) REVERT: A 184 ASP cc_start: 0.8169 (p0) cc_final: 0.7942 (p0) REVERT: A 186 TRP cc_start: 0.6942 (m-10) cc_final: 0.6717 (m-10) REVERT: A 190 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7342 (tm-30) REVERT: A 218 LEU cc_start: 0.8992 (mp) cc_final: 0.8703 (tt) REVERT: A 435 TYR cc_start: 0.7930 (t80) cc_final: 0.7575 (t80) REVERT: A 442 PHE cc_start: 0.6709 (m-80) cc_final: 0.6433 (m-80) REVERT: A 461 MET cc_start: 0.4842 (mpp) cc_final: 0.4301 (mmp) REVERT: A 487 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7715 (mmm160) REVERT: C 28 GLN cc_start: 0.8365 (pt0) cc_final: 0.7652 (pp30) REVERT: C 33 LEU cc_start: 0.9441 (tt) cc_final: 0.9080 (tp) REVERT: C 37 LEU cc_start: 0.9680 (mt) cc_final: 0.9327 (tp) REVERT: C 49 ILE cc_start: 0.9559 (mt) cc_final: 0.9310 (mm) REVERT: C 54 LYS cc_start: 0.8497 (mttt) cc_final: 0.7802 (mttp) REVERT: C 84 LYS cc_start: 0.9355 (mtpt) cc_final: 0.8817 (ttpt) REVERT: C 178 GLU cc_start: 0.8634 (mp0) cc_final: 0.8145 (mp0) REVERT: C 184 ASP cc_start: 0.8078 (p0) cc_final: 0.7763 (p0) REVERT: C 190 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7321 (tm-30) REVERT: C 218 LEU cc_start: 0.9086 (mp) cc_final: 0.8760 (tt) REVERT: C 338 ASP cc_start: 0.9342 (t0) cc_final: 0.9107 (t70) REVERT: C 347 MET cc_start: 0.8037 (ttp) cc_final: 0.7732 (tmm) REVERT: C 461 MET cc_start: 0.5318 (mpp) cc_final: 0.4788 (mmp) REVERT: C 487 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7661 (mmm160) REVERT: B 28 GLN cc_start: 0.8251 (pt0) cc_final: 0.7477 (pp30) REVERT: B 48 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8327 (mm-30) REVERT: B 54 LYS cc_start: 0.8583 (mttt) cc_final: 0.7922 (mttp) REVERT: B 56 GLU cc_start: 0.8718 (tp30) cc_final: 0.8371 (pm20) REVERT: B 84 LYS cc_start: 0.9356 (mtpt) cc_final: 0.8813 (ttpt) REVERT: B 138 MET cc_start: 0.8326 (mmt) cc_final: 0.7994 (mmt) REVERT: B 347 MET cc_start: 0.8095 (tpp) cc_final: 0.7741 (tpp) REVERT: B 410 GLU cc_start: 0.8717 (pm20) cc_final: 0.8360 (tm-30) REVERT: B 461 MET cc_start: 0.5369 (mpp) cc_final: 0.5012 (mmp) REVERT: B 567 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8030 (tm-30) REVERT: D 28 GLN cc_start: 0.8153 (pt0) cc_final: 0.7525 (pp30) REVERT: D 54 LYS cc_start: 0.8653 (mttt) cc_final: 0.7957 (mttp) REVERT: D 78 GLU cc_start: 0.8351 (tp30) cc_final: 0.7986 (tp30) REVERT: D 84 LYS cc_start: 0.9310 (mtpt) cc_final: 0.8817 (ttmt) REVERT: D 148 LYS cc_start: 0.8547 (ttpt) cc_final: 0.7915 (ttpt) REVERT: D 158 MET cc_start: 0.8611 (tmm) cc_final: 0.8142 (tmm) REVERT: D 165 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8294 (mptt) REVERT: D 178 GLU cc_start: 0.8720 (mp0) cc_final: 0.8340 (mp0) REVERT: D 184 ASP cc_start: 0.8226 (p0) cc_final: 0.7909 (p0) REVERT: D 190 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7463 (tm-30) REVERT: D 347 MET cc_start: 0.7811 (tpp) cc_final: 0.7559 (tpp) REVERT: D 366 HIS cc_start: 0.5973 (m-70) cc_final: 0.5294 (m-70) REVERT: D 461 MET cc_start: 0.5729 (mpp) cc_final: 0.5102 (mmp) REVERT: D 567 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8083 (tm-30) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2602 time to fit residues: 152.3959 Evaluate side-chains 305 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15320 Z= 0.266 Angle : 0.669 10.235 20640 Z= 0.341 Chirality : 0.042 0.140 2268 Planarity : 0.004 0.039 2596 Dihedral : 5.476 35.728 1976 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.26 (0.21), residues: 1760 helix: 0.98 (0.16), residues: 1120 sheet: -0.68 (0.75), residues: 56 loop : -1.27 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP B 186 HIS 0.009 0.001 HIS D 366 PHE 0.035 0.002 PHE A 229 TYR 0.028 0.002 TYR C 116 ARG 0.005 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.9290 (tpt) cc_final: 0.8698 (tpt) REVERT: A 28 GLN cc_start: 0.8318 (pt0) cc_final: 0.7566 (pp30) REVERT: A 31 CYS cc_start: 0.8338 (p) cc_final: 0.7703 (p) REVERT: A 54 LYS cc_start: 0.8665 (mttt) cc_final: 0.7907 (mttp) REVERT: A 84 LYS cc_start: 0.9365 (mtpt) cc_final: 0.8936 (ttmt) REVERT: A 122 GLU cc_start: 0.7668 (tp30) cc_final: 0.7442 (tm-30) REVERT: A 155 ASP cc_start: 0.7186 (t0) cc_final: 0.6688 (m-30) REVERT: A 158 MET cc_start: 0.8015 (tmm) cc_final: 0.7571 (tmm) REVERT: A 178 GLU cc_start: 0.8629 (mp0) cc_final: 0.8163 (mp0) REVERT: A 184 ASP cc_start: 0.8184 (p0) cc_final: 0.7851 (p0) REVERT: A 190 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7356 (tm-30) REVERT: A 338 ASP cc_start: 0.9380 (t0) cc_final: 0.8963 (t70) REVERT: A 347 MET cc_start: 0.8342 (tpp) cc_final: 0.8033 (tpp) REVERT: A 435 TYR cc_start: 0.8021 (t80) cc_final: 0.7682 (t80) REVERT: A 442 PHE cc_start: 0.6409 (m-80) cc_final: 0.6193 (m-80) REVERT: A 445 ILE cc_start: 0.8695 (pt) cc_final: 0.8492 (pt) REVERT: A 461 MET cc_start: 0.5173 (mpp) cc_final: 0.4835 (mmp) REVERT: A 487 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7733 (mmm160) REVERT: C 24 ILE cc_start: 0.8098 (mm) cc_final: 0.7824 (mt) REVERT: C 28 GLN cc_start: 0.8402 (pt0) cc_final: 0.7300 (pp30) REVERT: C 33 LEU cc_start: 0.9453 (tt) cc_final: 0.9171 (tp) REVERT: C 37 LEU cc_start: 0.9729 (mt) cc_final: 0.9371 (tp) REVERT: C 49 ILE cc_start: 0.9551 (mt) cc_final: 0.9324 (mm) REVERT: C 54 LYS cc_start: 0.8541 (mttt) cc_final: 0.7884 (mttp) REVERT: C 84 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9012 (ttpt) REVERT: C 122 GLU cc_start: 0.7730 (tp30) cc_final: 0.7441 (tm-30) REVERT: C 178 GLU cc_start: 0.8629 (mp0) cc_final: 0.8165 (mp0) REVERT: C 184 ASP cc_start: 0.8155 (p0) cc_final: 0.7936 (p0) REVERT: C 190 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7300 (tm-30) REVERT: C 338 ASP cc_start: 0.9327 (t0) cc_final: 0.9079 (t70) REVERT: C 410 GLU cc_start: 0.9045 (pm20) cc_final: 0.8274 (tm-30) REVERT: C 461 MET cc_start: 0.5964 (mpp) cc_final: 0.5540 (mmp) REVERT: C 487 ARG cc_start: 0.7931 (mmt90) cc_final: 0.7691 (mmm160) REVERT: B 28 GLN cc_start: 0.8276 (pt0) cc_final: 0.7463 (pp30) REVERT: B 33 LEU cc_start: 0.9566 (tp) cc_final: 0.9308 (tt) REVERT: B 37 LEU cc_start: 0.9623 (mt) cc_final: 0.9299 (tp) REVERT: B 54 LYS cc_start: 0.8658 (mttt) cc_final: 0.7896 (mttp) REVERT: B 84 LYS cc_start: 0.9321 (mtpt) cc_final: 0.8959 (ttpt) REVERT: B 138 MET cc_start: 0.8447 (mmt) cc_final: 0.8019 (mmt) REVERT: B 165 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8373 (mptt) REVERT: B 178 GLU cc_start: 0.8532 (mp0) cc_final: 0.7945 (mp0) REVERT: B 311 MET cc_start: 0.8407 (pmm) cc_final: 0.8206 (ptp) REVERT: B 347 MET cc_start: 0.8178 (tpp) cc_final: 0.7589 (tpp) REVERT: B 410 GLU cc_start: 0.8804 (pm20) cc_final: 0.8321 (tm-30) REVERT: B 435 TYR cc_start: 0.7720 (t80) cc_final: 0.7067 (t80) REVERT: B 461 MET cc_start: 0.5381 (mpp) cc_final: 0.4885 (mmp) REVERT: B 567 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7952 (tm-30) REVERT: D 28 GLN cc_start: 0.8203 (pt0) cc_final: 0.7549 (pp30) REVERT: D 54 LYS cc_start: 0.8658 (mttt) cc_final: 0.7911 (mttp) REVERT: D 84 LYS cc_start: 0.9319 (mtpt) cc_final: 0.8821 (ttmt) REVERT: D 92 TRP cc_start: 0.8922 (t60) cc_final: 0.8615 (t60) REVERT: D 148 LYS cc_start: 0.8522 (ttpt) cc_final: 0.7892 (ttpt) REVERT: D 158 MET cc_start: 0.8654 (tmm) cc_final: 0.8191 (tmm) REVERT: D 178 GLU cc_start: 0.8679 (mp0) cc_final: 0.8150 (mp0) REVERT: D 184 ASP cc_start: 0.8218 (p0) cc_final: 0.7933 (p0) REVERT: D 461 MET cc_start: 0.5788 (mpp) cc_final: 0.5263 (mmp) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.2562 time to fit residues: 142.4109 Evaluate side-chains 317 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 165 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15320 Z= 0.181 Angle : 0.629 10.000 20640 Z= 0.317 Chirality : 0.040 0.137 2268 Planarity : 0.004 0.045 2596 Dihedral : 5.245 34.491 1976 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.38 (0.21), residues: 1760 helix: 1.03 (0.16), residues: 1120 sheet: -0.57 (0.75), residues: 56 loop : -1.12 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 186 HIS 0.004 0.001 HIS C 366 PHE 0.020 0.001 PHE A 442 TYR 0.017 0.001 TYR C 116 ARG 0.005 0.000 ARG D 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8193 (pt0) cc_final: 0.7595 (pp30) REVERT: A 31 CYS cc_start: 0.8171 (p) cc_final: 0.7493 (p) REVERT: A 54 LYS cc_start: 0.8730 (mttt) cc_final: 0.7895 (mttp) REVERT: A 84 LYS cc_start: 0.9356 (mtpt) cc_final: 0.8891 (ttmt) REVERT: A 138 MET cc_start: 0.8206 (mmt) cc_final: 0.7810 (mmt) REVERT: A 155 ASP cc_start: 0.6945 (t0) cc_final: 0.6535 (m-30) REVERT: A 158 MET cc_start: 0.8052 (tmm) cc_final: 0.7606 (tmm) REVERT: A 178 GLU cc_start: 0.8639 (mp0) cc_final: 0.8172 (mp0) REVERT: A 184 ASP cc_start: 0.8082 (p0) cc_final: 0.7813 (p0) REVERT: A 190 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7343 (tm-30) REVERT: A 338 ASP cc_start: 0.9378 (t0) cc_final: 0.8977 (t0) REVERT: A 347 MET cc_start: 0.8171 (tpp) cc_final: 0.7935 (tpp) REVERT: A 435 TYR cc_start: 0.7897 (t80) cc_final: 0.7566 (t80) REVERT: A 445 ILE cc_start: 0.8660 (pt) cc_final: 0.8459 (pt) REVERT: A 461 MET cc_start: 0.5200 (mpp) cc_final: 0.4936 (mmp) REVERT: A 487 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7735 (mmm160) REVERT: C 24 ILE cc_start: 0.7969 (mm) cc_final: 0.7757 (mt) REVERT: C 28 GLN cc_start: 0.8348 (pt0) cc_final: 0.7604 (pp30) REVERT: C 33 LEU cc_start: 0.9396 (tt) cc_final: 0.9070 (tp) REVERT: C 37 LEU cc_start: 0.9670 (mt) cc_final: 0.9272 (tp) REVERT: C 54 LYS cc_start: 0.8537 (mttt) cc_final: 0.7855 (mttp) REVERT: C 84 LYS cc_start: 0.9365 (mtpt) cc_final: 0.8885 (ttmt) REVERT: C 122 GLU cc_start: 0.7668 (tp30) cc_final: 0.7290 (tm-30) REVERT: C 178 GLU cc_start: 0.8636 (mp0) cc_final: 0.8141 (mp0) REVERT: C 184 ASP cc_start: 0.8049 (p0) cc_final: 0.7763 (p0) REVERT: C 190 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7296 (tm-30) REVERT: C 347 MET cc_start: 0.8122 (tmm) cc_final: 0.7823 (tmm) REVERT: C 410 GLU cc_start: 0.9014 (pm20) cc_final: 0.8278 (tm-30) REVERT: C 461 MET cc_start: 0.5811 (mpp) cc_final: 0.5527 (mmp) REVERT: C 487 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7754 (mmm160) REVERT: B 28 GLN cc_start: 0.8291 (pt0) cc_final: 0.7455 (pp30) REVERT: B 54 LYS cc_start: 0.8364 (mttt) cc_final: 0.7845 (mttp) REVERT: B 78 GLU cc_start: 0.8379 (tp30) cc_final: 0.8070 (tp30) REVERT: B 84 LYS cc_start: 0.9359 (mtpt) cc_final: 0.8974 (ttpt) REVERT: B 138 MET cc_start: 0.8417 (mmt) cc_final: 0.8203 (mmt) REVERT: B 165 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8332 (mptt) REVERT: B 169 LEU cc_start: 0.9184 (mm) cc_final: 0.8972 (mm) REVERT: B 184 ASP cc_start: 0.8172 (p0) cc_final: 0.7735 (p0) REVERT: B 347 MET cc_start: 0.7983 (tpp) cc_final: 0.7725 (tpp) REVERT: B 410 GLU cc_start: 0.8787 (pm20) cc_final: 0.8338 (tm-30) REVERT: B 461 MET cc_start: 0.5362 (mpp) cc_final: 0.4894 (mmp) REVERT: B 567 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7969 (tm-30) REVERT: D 24 ILE cc_start: 0.7945 (mm) cc_final: 0.7694 (mt) REVERT: D 28 GLN cc_start: 0.8149 (pt0) cc_final: 0.7491 (pp30) REVERT: D 54 LYS cc_start: 0.8779 (mttt) cc_final: 0.7944 (mttp) REVERT: D 84 LYS cc_start: 0.9322 (mtpt) cc_final: 0.8855 (ttmt) REVERT: D 92 TRP cc_start: 0.8884 (t60) cc_final: 0.8651 (t60) REVERT: D 148 LYS cc_start: 0.8535 (ttpt) cc_final: 0.7949 (ttpt) REVERT: D 155 ASP cc_start: 0.7163 (t0) cc_final: 0.6841 (m-30) REVERT: D 158 MET cc_start: 0.8655 (tmm) cc_final: 0.8121 (tmm) REVERT: D 165 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8312 (mptt) REVERT: D 178 GLU cc_start: 0.8676 (mp0) cc_final: 0.8214 (mp0) REVERT: D 184 ASP cc_start: 0.8098 (p0) cc_final: 0.7755 (p0) REVERT: D 338 ASP cc_start: 0.9327 (t0) cc_final: 0.9055 (t70) REVERT: D 461 MET cc_start: 0.5823 (mpp) cc_final: 0.5321 (mmp) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2503 time to fit residues: 140.9121 Evaluate side-chains 319 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15320 Z= 0.205 Angle : 0.634 9.728 20640 Z= 0.319 Chirality : 0.041 0.166 2268 Planarity : 0.004 0.043 2596 Dihedral : 5.239 34.409 1976 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1760 helix: 1.01 (0.16), residues: 1120 sheet: -0.78 (0.74), residues: 56 loop : -1.12 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 186 HIS 0.005 0.001 HIS C 366 PHE 0.019 0.001 PHE A 475 TYR 0.017 0.001 TYR C 116 ARG 0.004 0.000 ARG D 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8201 (pt0) cc_final: 0.7582 (pp30) REVERT: A 31 CYS cc_start: 0.8190 (p) cc_final: 0.7541 (p) REVERT: A 54 LYS cc_start: 0.8728 (mttt) cc_final: 0.7886 (mttp) REVERT: A 84 LYS cc_start: 0.9361 (mtpt) cc_final: 0.8926 (ttmt) REVERT: A 138 MET cc_start: 0.8288 (mmt) cc_final: 0.7909 (mmt) REVERT: A 155 ASP cc_start: 0.6988 (t0) cc_final: 0.6616 (m-30) REVERT: A 158 MET cc_start: 0.8095 (tmm) cc_final: 0.7609 (tmm) REVERT: A 178 GLU cc_start: 0.8608 (mp0) cc_final: 0.8168 (mp0) REVERT: A 184 ASP cc_start: 0.8115 (p0) cc_final: 0.7887 (p0) REVERT: A 190 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7336 (tm-30) REVERT: A 338 ASP cc_start: 0.9389 (t0) cc_final: 0.8984 (t70) REVERT: A 435 TYR cc_start: 0.8019 (t80) cc_final: 0.7676 (t80) REVERT: A 461 MET cc_start: 0.5454 (mpp) cc_final: 0.5114 (mmp) REVERT: A 487 ARG cc_start: 0.8098 (mmt90) cc_final: 0.7832 (mmm160) REVERT: C 24 ILE cc_start: 0.7978 (mm) cc_final: 0.7723 (mt) REVERT: C 28 GLN cc_start: 0.8337 (pt0) cc_final: 0.7269 (pp30) REVERT: C 33 LEU cc_start: 0.9414 (tt) cc_final: 0.9103 (tp) REVERT: C 37 LEU cc_start: 0.9696 (mt) cc_final: 0.9316 (tp) REVERT: C 54 LYS cc_start: 0.8633 (mttt) cc_final: 0.7846 (mttp) REVERT: C 84 LYS cc_start: 0.9368 (mtpt) cc_final: 0.8883 (ttmt) REVERT: C 122 GLU cc_start: 0.7637 (tp30) cc_final: 0.7300 (tm-30) REVERT: C 178 GLU cc_start: 0.8633 (mp0) cc_final: 0.8157 (mp0) REVERT: C 184 ASP cc_start: 0.8086 (p0) cc_final: 0.7882 (p0) REVERT: C 190 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7287 (tm-30) REVERT: C 347 MET cc_start: 0.8118 (tmm) cc_final: 0.7788 (tmm) REVERT: C 410 GLU cc_start: 0.9055 (pm20) cc_final: 0.8284 (tm-30) REVERT: C 461 MET cc_start: 0.6268 (mpp) cc_final: 0.6034 (mmp) REVERT: C 464 ASN cc_start: 0.7733 (t0) cc_final: 0.6714 (t0) REVERT: C 487 ARG cc_start: 0.7970 (mmt90) cc_final: 0.7733 (mmm160) REVERT: B 24 ILE cc_start: 0.8068 (mm) cc_final: 0.7823 (mm) REVERT: B 28 GLN cc_start: 0.8305 (pt0) cc_final: 0.7513 (pp30) REVERT: B 31 CYS cc_start: 0.8475 (p) cc_final: 0.8013 (p) REVERT: B 54 LYS cc_start: 0.8393 (mttt) cc_final: 0.7774 (mttp) REVERT: B 84 LYS cc_start: 0.9361 (mtpt) cc_final: 0.8970 (ttpt) REVERT: B 138 MET cc_start: 0.8481 (mmt) cc_final: 0.8272 (mmm) REVERT: B 165 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8345 (mptt) REVERT: B 178 GLU cc_start: 0.8532 (mp0) cc_final: 0.8013 (mp0) REVERT: B 347 MET cc_start: 0.7966 (tpp) cc_final: 0.7711 (tpp) REVERT: B 363 MET cc_start: 0.7558 (mtp) cc_final: 0.7338 (mtm) REVERT: B 410 GLU cc_start: 0.8798 (pm20) cc_final: 0.8329 (tm-30) REVERT: B 435 TYR cc_start: 0.7806 (t80) cc_final: 0.7481 (t80) REVERT: B 461 MET cc_start: 0.5571 (mpp) cc_final: 0.5067 (mmp) REVERT: B 567 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7924 (tm-30) REVERT: D 24 ILE cc_start: 0.7877 (mm) cc_final: 0.7641 (mt) REVERT: D 28 GLN cc_start: 0.8169 (pt0) cc_final: 0.7538 (pp30) REVERT: D 54 LYS cc_start: 0.8745 (mttt) cc_final: 0.7858 (mttp) REVERT: D 84 LYS cc_start: 0.9340 (mtpt) cc_final: 0.8868 (ttmt) REVERT: D 92 TRP cc_start: 0.8877 (t60) cc_final: 0.8624 (t60) REVERT: D 148 LYS cc_start: 0.8477 (ttpt) cc_final: 0.7799 (ttpt) REVERT: D 155 ASP cc_start: 0.7161 (t0) cc_final: 0.6870 (m-30) REVERT: D 158 MET cc_start: 0.8661 (tmm) cc_final: 0.8253 (tmm) REVERT: D 165 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8268 (mptt) REVERT: D 178 GLU cc_start: 0.8641 (mp0) cc_final: 0.8067 (mp0) REVERT: D 338 ASP cc_start: 0.9338 (t0) cc_final: 0.8943 (t70) REVERT: D 461 MET cc_start: 0.5854 (mpp) cc_final: 0.5385 (mmp) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2619 time to fit residues: 146.1404 Evaluate side-chains 314 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 150 optimal weight: 0.0040 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 0.0570 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.109030 restraints weight = 33269.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111289 restraints weight = 22243.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112859 restraints weight = 16826.756| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15320 Z= 0.172 Angle : 0.617 9.629 20640 Z= 0.312 Chirality : 0.040 0.146 2268 Planarity : 0.004 0.045 2596 Dihedral : 5.113 33.177 1976 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1760 helix: 1.06 (0.16), residues: 1092 sheet: -0.64 (0.74), residues: 56 loop : -1.09 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 186 HIS 0.008 0.001 HIS A 430 PHE 0.028 0.001 PHE C 499 TYR 0.016 0.001 TYR C 116 ARG 0.004 0.000 ARG D 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.48 seconds wall clock time: 64 minutes 40.24 seconds (3880.24 seconds total)