Starting phenix.real_space_refine on Sun Mar 17 20:47:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj1_33216/03_2024/7xj1_33216_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj1_33216/03_2024/7xj1_33216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj1_33216/03_2024/7xj1_33216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj1_33216/03_2024/7xj1_33216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj1_33216/03_2024/7xj1_33216_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj1_33216/03_2024/7xj1_33216_updated.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.103 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: 5 Type Number sf(0) Gaussians S 120 5.16 5 C 12467 2.51 5 N 3129 2.21 5 O 3164 1.98 5 F 30 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 641": "OD1" <-> "OD2" Residue "B PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C ASP 396": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "C TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ASP 340": "OD1" <-> "OD2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 586": "OD1" <-> "OD2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D ASP 641": "OD1" <-> "OD2" Residue "D PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 687": "OE1" <-> "OE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18910 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4593 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 13, 'TRANS': 592} Chain breaks: 4 Unresolved non-hydrogen bonds: 343 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 242 Chain: "C" Number of atoms: 4647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4647 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 14, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 261 Chain: "A" Number of atoms: 4641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4641 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 14, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 264 Chain: "D" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4570 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 13, 'TRANS': 592} Chain breaks: 4 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 250 Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Unusual residues: {'6OU': 3, 'EQK': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 139 Unusual residues: {'6OU': 3, 'EQK': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {'6OU': 2, 'EQK': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {'6OU': 2, 'EQK': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 10.17, per 1000 atoms: 0.54 Number of scatterers: 18910 At special positions: 0 Unit cell: (149.76, 146.64, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 F 30 9.00 O 3164 8.00 N 3129 7.00 C 12467 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: 7.38 Conformation dependent library (CDL) restraints added in 3.4 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 4 sheets defined 56.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.673A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 327 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 460 removed outlier: 4.248A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 506 Processing helix chain 'B' and resid 522 through 541 Processing helix chain 'B' and resid 547 through 563 removed outlier: 4.661A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 581 removed outlier: 4.309A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 651 through 677 Processing helix chain 'B' and resid 681 through 706 Processing helix chain 'B' and resid 709 through 715 Processing helix chain 'C' and resid 120 through 129 Processing helix chain 'C' and resid 133 through 148 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.650A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 310 through 313 No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 416 through 419 No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 460 removed outlier: 5.539A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 506 Processing helix chain 'C' and resid 519 through 541 removed outlier: 3.846A pdb=" N PHE C 526 " --> pdb=" O HIS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 566 removed outlier: 4.549A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 607 removed outlier: 4.514A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 651 through 679 Processing helix chain 'C' and resid 683 through 706 removed outlier: 4.319A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 133 through 148 Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.615A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 370 through 373 Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 416 through 419 No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 460 removed outlier: 5.533A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N HIS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 506 Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.735A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 566 removed outlier: 4.576A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 607 removed outlier: 4.532A pdb=" N MET A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 651 through 679 Processing helix chain 'A' and resid 683 through 706 removed outlier: 4.289A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 715 Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 184 through 197 removed outlier: 3.641A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 316 through 327 Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 403 through 409 Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 460 removed outlier: 4.242A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 506 removed outlier: 4.300A pdb=" N VAL D 490 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D 492 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU D 501 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 Processing helix chain 'D' and resid 547 through 563 removed outlier: 4.655A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 5.063A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 4.102A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 651 through 677 Processing helix chain 'D' and resid 681 through 706 Processing helix chain 'D' and resid 709 through 715 Processing sheet with id= A, first strand: chain 'B' and resid 376 through 378 Processing sheet with id= B, first strand: chain 'C' and resid 385 through 391 Processing sheet with id= C, first strand: chain 'A' and resid 385 through 391 Processing sheet with id= D, first strand: chain 'D' and resid 376 through 378 970 hydrogen bonds defined for protein. 2781 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: 5.43 Time building geometry restraints manager: 8.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 2831 1.26 - 1.40: 4984 1.40 - 1.54: 10981 1.54 - 1.67: 334 1.67 - 1.81: 186 Bond restraints: 19316 Sorted by residual: bond pdb=" C20 EQK D1103 " pdb=" S01 EQK D1103 " ideal model delta sigma weight residual 1.732 1.505 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C20 EQK B1602 " pdb=" S01 EQK B1602 " ideal model delta sigma weight residual 1.732 1.506 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C20 EQK A1801 " pdb=" S01 EQK A1801 " ideal model delta sigma weight residual 1.732 1.508 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C20 EQK C1106 " pdb=" S01 EQK C1106 " ideal model delta sigma weight residual 1.732 1.508 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C20 EQK A1802 " pdb=" S01 EQK A1802 " ideal model delta sigma weight residual 1.732 1.510 0.222 2.00e-02 2.50e+03 1.24e+02 ... (remaining 19311 not shown) Histogram of bond angle deviations from ideal: 99.16 - 115.32: 12176 115.32 - 131.49: 14055 131.49 - 147.65: 40 147.65 - 163.81: 0 163.81 - 179.97: 10 Bond angle restraints: 26281 Sorted by residual: angle pdb=" C20 EQK A1805 " pdb=" S01 EQK A1805 " pdb=" C25 EQK A1805 " ideal model delta sigma weight residual 88.77 108.01 -19.24 3.00e+00 1.11e-01 4.11e+01 angle pdb=" C20 EQK C1101 " pdb=" S01 EQK C1101 " pdb=" C25 EQK C1101 " ideal model delta sigma weight residual 88.77 107.75 -18.98 3.00e+00 1.11e-01 4.00e+01 angle pdb=" C20 EQK B1603 " pdb=" S01 EQK B1603 " pdb=" C25 EQK B1603 " ideal model delta sigma weight residual 88.77 107.68 -18.91 3.00e+00 1.11e-01 3.97e+01 angle pdb=" C20 EQK D1101 " pdb=" S01 EQK D1101 " pdb=" C25 EQK D1101 " ideal model delta sigma weight residual 88.77 107.39 -18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" C20 EQK D1103 " pdb=" S01 EQK D1103 " pdb=" C25 EQK D1103 " ideal model delta sigma weight residual 88.77 106.95 -18.18 3.00e+00 1.11e-01 3.67e+01 ... (remaining 26276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.46: 9932 18.46 - 36.91: 1080 36.91 - 55.37: 279 55.37 - 73.82: 67 73.82 - 92.28: 31 Dihedral angle restraints: 11389 sinusoidal: 4199 harmonic: 7190 Sorted by residual: dihedral pdb=" CA THR B 680 " pdb=" C THR B 680 " pdb=" N VAL B 681 " pdb=" CA VAL B 681 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLY D 678 " pdb=" C GLY D 678 " pdb=" N GLU D 679 " pdb=" CA GLU D 679 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA THR D 680 " pdb=" C THR D 680 " pdb=" N VAL D 681 " pdb=" CA VAL D 681 " ideal model delta harmonic sigma weight residual -180.00 -153.47 -26.53 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 11386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2883 0.072 - 0.143: 196 0.143 - 0.215: 9 0.215 - 0.287: 2 0.287 - 0.358: 2 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CA TRP C 739 " pdb=" N TRP C 739 " pdb=" C TRP C 739 " pdb=" CB TRP C 739 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA PHE C 522 " pdb=" N PHE C 522 " pdb=" C PHE C 522 " pdb=" CB PHE C 522 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA ILE C 516 " pdb=" N ILE C 516 " pdb=" C ILE C 516 " pdb=" CB ILE C 516 " both_signs ideal model delta sigma weight residual False 2.43 2.18 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 3089 not shown) Planarity restraints: 3199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 403 " 0.014 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C VAL B 403 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL B 403 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU B 404 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 403 " -0.014 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C VAL D 403 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL D 403 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU D 404 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 583 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C ILE A 583 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE A 583 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 584 " 0.014 2.00e-02 2.50e+03 ... (remaining 3196 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1940 2.74 - 3.28: 19198 3.28 - 3.82: 31854 3.82 - 4.36: 38761 4.36 - 4.90: 66441 Nonbonded interactions: 158194 Sorted by model distance: nonbonded pdb=" O GLU A 682 " pdb=" OG SER A 685 " model vdw 2.200 2.440 nonbonded pdb=" NH1 ARG D 567 " pdb=" OE1 GLN D 695 " model vdw 2.208 2.520 nonbonded pdb=" NH1 ARG D 363 " pdb=" O LEU D 373 " model vdw 2.212 2.520 nonbonded pdb=" O LYS C 545 " pdb=" OH TYR D 650 " model vdw 2.218 2.440 nonbonded pdb=" NH1 ARG B 363 " pdb=" O LEU B 373 " model vdw 2.220 2.520 ... (remaining 158189 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' and (resid 118 through 464 or resid 484 through 508 or resid 515 thro \ ugh 518 or (resid 519 through 520 and (name N or name CA or name C or name O or \ name CB )) or resid 521 through 582 or (resid 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 648 or (resid 649 and (name N or \ name CA or name C or name O or name CB )) or resid 650 through 681 or (resid 68 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 683 through \ 716 or (resid 717 and (name N or name CA or name C or name O or name CB or name \ CG or name SD )) or resid 718 through 754 or resid 1804)) selection = (chain 'B' and ((resid 118 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 through 410 or (resid 411 through 412 and (name N o \ r name CA or name C or name O or name CB )) or resid 413 through 644 or (resid 6 \ 45 and (name N or name CA or name C or name O or name CB )) or resid 646 through \ 676 or (resid 677 and (name N or name CA or name C or name O or name CB )) or r \ esid 678 through 716 or (resid 717 and (name N or name CA or name C or name O or \ name CB or name CG or name SD )) or resid 718 through 734 or (resid 735 through \ 736 and (name N or name CA or name C or name O or name CB )) or resid 737 throu \ gh 754 or resid 1604)) selection = (chain 'C' and (resid 118 through 464 or resid 484 through 508 or resid 515 thro \ ugh 518 or (resid 519 through 520 and (name N or name CA or name C or name O or \ name CB )) or resid 521 through 582 or (resid 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 648 or (resid 649 and (name N or \ name CA or name C or name O or name CB )) or resid 650 through 681 or (resid 68 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 683 through \ 734 or (resid 735 through 736 and (name N or name CA or name C or name O or name \ CB )) or resid 737 or (resid 738 and (name N or name CA or name C or name O or \ name CB )) or resid 739 through 754 or resid 1104)) selection = (chain 'D' and (resid 118 through 518 or (resid 519 through 520 and (name N or n \ ame CA or name C or name O or name CB )) or resid 521 through 644 or (resid 645 \ and (name N or name CA or name C or name O or name CB )) or resid 646 through 67 \ 6 or (resid 677 and (name N or name CA or name C or name O or name CB )) or resi \ d 678 through 754 or resid 1104)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 7.690 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 49.970 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.015 0.227 19316 Z= 0.926 Angle : 0.955 19.237 26281 Z= 0.457 Chirality : 0.041 0.358 3092 Planarity : 0.004 0.041 3199 Dihedral : 17.487 92.280 6713 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.02 % Allowed : 19.78 % Favored : 76.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.14), residues: 2408 helix: -1.72 (0.11), residues: 1582 sheet: -2.22 (0.59), residues: 64 loop : -3.12 (0.18), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 380 HIS 0.009 0.001 HIS D 301 PHE 0.014 0.001 PHE B 316 TYR 0.021 0.002 TYR C 451 ARG 0.006 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 397 time to evaluate : 2.236 Fit side-chains REVERT: B 160 HIS cc_start: 0.6798 (m-70) cc_final: 0.6584 (m90) REVERT: B 358 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8205 (tttm) REVERT: B 371 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7889 (tpp80) REVERT: B 447 PHE cc_start: 0.8074 (m-80) cc_final: 0.7824 (m-10) REVERT: B 485 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6944 (mm) REVERT: B 487 ARG cc_start: 0.7880 (mtt90) cc_final: 0.5857 (ttt180) REVERT: B 492 ILE cc_start: 0.8896 (mp) cc_final: 0.8600 (mp) REVERT: B 516 ILE cc_start: 0.7890 (mt) cc_final: 0.7470 (pp) REVERT: B 521 TRP cc_start: 0.8281 (t-100) cc_final: 0.8039 (t-100) REVERT: B 631 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7172 (mm-30) REVERT: B 668 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8343 (mp) REVERT: B 672 MET cc_start: 0.7880 (tmm) cc_final: 0.7524 (ttt) REVERT: B 712 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7548 (mtm180) REVERT: C 214 GLU cc_start: 0.8033 (tt0) cc_final: 0.7815 (tt0) REVERT: C 240 ASP cc_start: 0.7773 (p0) cc_final: 0.7495 (p0) REVERT: C 288 ASP cc_start: 0.8293 (t0) cc_final: 0.8015 (t0) REVERT: C 378 THR cc_start: 0.8116 (m) cc_final: 0.7710 (m) REVERT: C 483 GLN cc_start: 0.6212 (tm-30) cc_final: 0.5816 (tm130) REVERT: A 213 TYR cc_start: 0.8306 (m-80) cc_final: 0.8003 (m-80) REVERT: A 214 GLU cc_start: 0.8073 (tt0) cc_final: 0.7861 (tt0) REVERT: A 240 ASP cc_start: 0.7820 (p0) cc_final: 0.7414 (p0) REVERT: A 378 THR cc_start: 0.8217 (m) cc_final: 0.7845 (m) REVERT: A 690 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7230 (ttp-110) REVERT: D 358 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8233 (tttm) REVERT: D 371 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7939 (tpp80) REVERT: D 447 PHE cc_start: 0.8014 (m-80) cc_final: 0.7752 (m-10) REVERT: D 516 ILE cc_start: 0.7950 (mt) cc_final: 0.7487 (pp) REVERT: D 546 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7361 (tp30) REVERT: D 631 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7183 (mm-30) REVERT: D 712 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7563 (mtm180) outliers start: 71 outliers final: 30 residues processed: 454 average time/residue: 1.0482 time to fit residues: 544.7081 Evaluate side-chains 327 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 295 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS B 301 HIS B 647 ASN B 671 ASN C 180 ASN C 197 ASN C 205 ASN C 279 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN C 410 ASN C 483 GLN C 580 GLN A 180 ASN A 197 ASN A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 410 ASN A 570 GLN A 580 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN D 284 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN D 647 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19316 Z= 0.204 Angle : 0.566 9.594 26281 Z= 0.292 Chirality : 0.037 0.126 3092 Planarity : 0.004 0.040 3199 Dihedral : 13.072 88.682 3010 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.44 % Allowed : 22.45 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2408 helix: -0.45 (0.12), residues: 1592 sheet: -1.68 (0.60), residues: 64 loop : -2.57 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 380 HIS 0.008 0.001 HIS D 301 PHE 0.020 0.001 PHE B 445 TYR 0.016 0.001 TYR C 451 ARG 0.007 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 317 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 HIS cc_start: 0.6749 (m-70) cc_final: 0.6524 (m90) REVERT: B 358 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8199 (tttm) REVERT: B 447 PHE cc_start: 0.8099 (m-80) cc_final: 0.7790 (m-10) REVERT: B 487 ARG cc_start: 0.7744 (mtt90) cc_final: 0.5919 (ttt180) REVERT: B 492 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 516 ILE cc_start: 0.8150 (mt) cc_final: 0.7707 (pp) REVERT: B 611 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7711 (ttmm) REVERT: B 631 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 668 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8318 (mp) REVERT: B 687 GLU cc_start: 0.7158 (tp30) cc_final: 0.6955 (tp30) REVERT: B 712 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7592 (mtm180) REVERT: C 483 GLN cc_start: 0.6204 (tm130) cc_final: 0.5739 (tm130) REVERT: A 214 GLU cc_start: 0.7995 (tt0) cc_final: 0.7771 (tt0) REVERT: A 378 THR cc_start: 0.8210 (m) cc_final: 0.7840 (m) REVERT: A 483 GLN cc_start: 0.5808 (tm130) cc_final: 0.5551 (tm130) REVERT: A 690 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7273 (ttp-110) REVERT: A 694 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8509 (mp) REVERT: D 358 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8218 (tttm) REVERT: D 371 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7922 (tpp80) REVERT: D 447 PHE cc_start: 0.8139 (m-80) cc_final: 0.7831 (m-10) REVERT: D 516 ILE cc_start: 0.8058 (mt) cc_final: 0.7576 (pp) REVERT: D 546 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7323 (tp30) REVERT: D 631 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7228 (mm-30) REVERT: D 690 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7590 (mtm110) REVERT: D 712 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7591 (mtm180) outliers start: 96 outliers final: 40 residues processed: 378 average time/residue: 1.0435 time to fit residues: 453.0849 Evaluate side-chains 335 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 292 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 237 optimal weight: 0.6980 chunk 196 optimal weight: 0.7980 chunk 218 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN B 273 ASN C 279 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19316 Z= 0.207 Angle : 0.560 8.735 26281 Z= 0.288 Chirality : 0.037 0.122 3092 Planarity : 0.004 0.052 3199 Dihedral : 12.836 87.653 2982 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.99 % Allowed : 23.87 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2408 helix: -0.01 (0.13), residues: 1580 sheet: -1.47 (0.61), residues: 64 loop : -2.38 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 380 HIS 0.008 0.001 HIS D 301 PHE 0.014 0.001 PHE D 449 TYR 0.017 0.001 TYR C 451 ARG 0.006 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 302 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 HIS cc_start: 0.6764 (m-70) cc_final: 0.6533 (m90) REVERT: B 358 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8190 (tttm) REVERT: B 447 PHE cc_start: 0.8096 (m-80) cc_final: 0.7795 (m-10) REVERT: B 487 ARG cc_start: 0.7709 (mtt90) cc_final: 0.5889 (ttt180) REVERT: B 492 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 516 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7633 (pp) REVERT: B 546 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7454 (tp30) REVERT: B 611 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7712 (ttmm) REVERT: B 631 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7166 (mm-30) REVERT: B 687 GLU cc_start: 0.7118 (tp30) cc_final: 0.6909 (tp30) REVERT: B 712 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7611 (mtm180) REVERT: B 717 MET cc_start: 0.7524 (mpp) cc_final: 0.6875 (mpp) REVERT: C 240 ASP cc_start: 0.7943 (p0) cc_final: 0.7624 (p0) REVERT: C 288 ASP cc_start: 0.8308 (t0) cc_final: 0.8006 (t0) REVERT: C 378 THR cc_start: 0.8072 (m) cc_final: 0.7675 (m) REVERT: C 483 GLN cc_start: 0.6370 (tm130) cc_final: 0.5925 (tm130) REVERT: C 694 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 702 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: A 213 TYR cc_start: 0.8214 (m-80) cc_final: 0.7927 (m-80) REVERT: A 214 GLU cc_start: 0.7993 (tt0) cc_final: 0.7766 (tt0) REVERT: A 378 THR cc_start: 0.8205 (m) cc_final: 0.7838 (m) REVERT: A 484 LEU cc_start: 0.7077 (mt) cc_final: 0.6753 (mm) REVERT: A 513 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8458 (mt) REVERT: A 687 GLU cc_start: 0.7473 (tp30) cc_final: 0.7170 (tp30) REVERT: A 702 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: D 358 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8209 (tttm) REVERT: D 371 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7968 (tpp80) REVERT: D 447 PHE cc_start: 0.8132 (m-80) cc_final: 0.7832 (m-10) REVERT: D 516 ILE cc_start: 0.7994 (mt) cc_final: 0.7520 (pp) REVERT: D 546 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7316 (tp30) REVERT: D 631 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7169 (mm-30) REVERT: D 690 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7539 (mtm110) REVERT: D 712 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7596 (mtm180) outliers start: 88 outliers final: 42 residues processed: 349 average time/residue: 1.1057 time to fit residues: 441.4042 Evaluate side-chains 336 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 287 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 690 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 233 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19316 Z= 0.207 Angle : 0.560 8.735 26281 Z= 0.288 Chirality : 0.037 0.122 3092 Planarity : 0.004 0.052 3199 Dihedral : 12.808 87.653 2980 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.78 % Allowed : 27.27 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2408 helix: -0.01 (0.13), residues: 1580 sheet: -1.47 (0.61), residues: 64 loop : -2.38 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 380 HIS 0.008 0.001 HIS D 301 PHE 0.014 0.001 PHE D 449 TYR 0.017 0.001 TYR C 451 ARG 0.006 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 287 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 HIS cc_start: 0.6765 (m-70) cc_final: 0.6533 (m90) REVERT: B 358 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8190 (tttm) REVERT: B 447 PHE cc_start: 0.8095 (m-80) cc_final: 0.7795 (m-10) REVERT: B 487 ARG cc_start: 0.7709 (mtt90) cc_final: 0.5889 (ttt180) REVERT: B 492 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 516 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7633 (pp) REVERT: B 546 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7453 (tp30) REVERT: B 611 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7713 (ttmm) REVERT: B 631 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7163 (mm-30) REVERT: B 712 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7611 (mtm180) REVERT: B 717 MET cc_start: 0.7532 (mpp) cc_final: 0.6875 (mpp) REVERT: C 240 ASP cc_start: 0.7916 (p0) cc_final: 0.7624 (p0) REVERT: C 288 ASP cc_start: 0.8309 (t0) cc_final: 0.8005 (t0) REVERT: C 378 THR cc_start: 0.8072 (m) cc_final: 0.7675 (m) REVERT: C 483 GLN cc_start: 0.6368 (tm130) cc_final: 0.5925 (tm130) REVERT: C 694 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 702 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: A 213 TYR cc_start: 0.8213 (m-80) cc_final: 0.7927 (m-80) REVERT: A 214 GLU cc_start: 0.7993 (tt0) cc_final: 0.7766 (tt0) REVERT: A 378 THR cc_start: 0.8206 (m) cc_final: 0.7838 (m) REVERT: A 513 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8458 (mt) REVERT: A 687 GLU cc_start: 0.7481 (tp30) cc_final: 0.7189 (tp30) REVERT: A 702 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: D 358 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8209 (tttm) REVERT: D 371 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7968 (tpp80) REVERT: D 447 PHE cc_start: 0.8130 (m-80) cc_final: 0.7832 (m-10) REVERT: D 516 ILE cc_start: 0.7988 (mt) cc_final: 0.7520 (pp) REVERT: D 546 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7316 (tp30) REVERT: D 631 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7168 (mm-30) REVERT: D 690 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7539 (mtm110) REVERT: D 712 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7596 (mtm180) outliers start: 49 outliers final: 42 residues processed: 309 average time/residue: 1.1476 time to fit residues: 403.4168 Evaluate side-chains 335 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 286 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 690 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 199 optimal weight: 0.1980 chunk 161 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 209 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19316 Z= 0.217 Angle : 0.540 6.079 26281 Z= 0.279 Chirality : 0.037 0.141 3092 Planarity : 0.004 0.052 3199 Dihedral : 12.498 88.394 2980 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.90 % Allowed : 23.70 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2408 helix: 0.30 (0.13), residues: 1578 sheet: -1.21 (0.61), residues: 64 loop : -2.18 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 380 HIS 0.008 0.001 HIS D 301 PHE 0.017 0.001 PHE C 489 TYR 0.017 0.001 TYR C 451 ARG 0.008 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 301 time to evaluate : 2.158 Fit side-chains revert: symmetry clash REVERT: B 160 HIS cc_start: 0.6809 (m-70) cc_final: 0.6535 (m90) REVERT: B 358 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8184 (tttm) REVERT: B 447 PHE cc_start: 0.8095 (m-80) cc_final: 0.7818 (m-10) REVERT: B 487 ARG cc_start: 0.7706 (mtt90) cc_final: 0.5906 (ttt180) REVERT: B 492 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8525 (mp) REVERT: B 516 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7636 (pp) REVERT: B 546 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7347 (tp30) REVERT: B 631 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 712 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7619 (mtm180) REVERT: B 717 MET cc_start: 0.7482 (mpp) cc_final: 0.6769 (mpp) REVERT: C 288 ASP cc_start: 0.8317 (t0) cc_final: 0.8011 (t0) REVERT: C 378 THR cc_start: 0.8057 (m) cc_final: 0.7671 (m) REVERT: C 483 GLN cc_start: 0.6390 (tm130) cc_final: 0.5936 (tm130) REVERT: C 694 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 702 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6808 (mt-10) REVERT: A 213 TYR cc_start: 0.8206 (m-80) cc_final: 0.7859 (m-80) REVERT: A 214 GLU cc_start: 0.7980 (tt0) cc_final: 0.7744 (tt0) REVERT: A 378 THR cc_start: 0.8195 (m) cc_final: 0.7824 (m) REVERT: A 513 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 687 GLU cc_start: 0.7492 (tp30) cc_final: 0.7209 (tp30) REVERT: A 694 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 702 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: D 358 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8201 (tttm) REVERT: D 447 PHE cc_start: 0.8117 (m-80) cc_final: 0.7836 (m-10) REVERT: D 516 ILE cc_start: 0.7919 (mt) cc_final: 0.7476 (pp) REVERT: D 589 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7417 (mmtm) REVERT: D 631 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7232 (mm-30) REVERT: D 712 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7607 (mtm180) outliers start: 104 outliers final: 49 residues processed: 363 average time/residue: 1.0713 time to fit residues: 446.1291 Evaluate side-chains 351 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 294 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 57 optimal weight: 0.0570 chunk 234 optimal weight: 0.0980 chunk 194 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 410 ASN A 570 GLN D 426 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19316 Z= 0.155 Angle : 0.522 5.988 26281 Z= 0.272 Chirality : 0.036 0.139 3092 Planarity : 0.004 0.071 3199 Dihedral : 12.164 88.448 2978 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.44 % Allowed : 24.43 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2408 helix: 0.55 (0.13), residues: 1578 sheet: -1.00 (0.62), residues: 64 loop : -2.13 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 380 HIS 0.005 0.001 HIS B 301 PHE 0.010 0.001 PHE C 666 TYR 0.015 0.001 TYR C 451 ARG 0.011 0.001 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 311 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 HIS cc_start: 0.6811 (m-70) cc_final: 0.6609 (m90) REVERT: B 358 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8170 (tttm) REVERT: B 446 CYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7534 (m) REVERT: B 447 PHE cc_start: 0.8082 (m-80) cc_final: 0.7780 (m-10) REVERT: B 487 ARG cc_start: 0.7645 (mtt90) cc_final: 0.5919 (ttt90) REVERT: B 492 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 516 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7601 (pp) REVERT: B 546 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7291 (tp30) REVERT: B 570 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: B 611 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7585 (ttmt) REVERT: B 631 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 712 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7611 (mtm180) REVERT: B 717 MET cc_start: 0.7391 (mpp) cc_final: 0.6722 (mpp) REVERT: C 288 ASP cc_start: 0.8308 (t0) cc_final: 0.7997 (t0) REVERT: C 378 THR cc_start: 0.8011 (m) cc_final: 0.7620 (m) REVERT: C 483 GLN cc_start: 0.6249 (tm130) cc_final: 0.5697 (tm130) REVERT: C 690 ARG cc_start: 0.7531 (ttm110) cc_final: 0.7093 (ttp-110) REVERT: C 694 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8408 (mp) REVERT: C 702 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: A 213 TYR cc_start: 0.8194 (m-80) cc_final: 0.7851 (m-80) REVERT: A 214 GLU cc_start: 0.7943 (tt0) cc_final: 0.7708 (tt0) REVERT: A 378 THR cc_start: 0.8156 (m) cc_final: 0.7788 (m) REVERT: A 513 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8396 (mt) REVERT: A 687 GLU cc_start: 0.7479 (tp30) cc_final: 0.7205 (tp30) REVERT: A 694 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 702 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6771 (mt-10) REVERT: D 358 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8185 (tttm) REVERT: D 446 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7563 (m) REVERT: D 447 PHE cc_start: 0.8104 (m-80) cc_final: 0.7795 (m-10) REVERT: D 492 ILE cc_start: 0.8555 (mp) cc_final: 0.8338 (mp) REVERT: D 516 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7466 (pp) REVERT: D 546 GLU cc_start: 0.6834 (tp30) cc_final: 0.6605 (tp30) REVERT: D 631 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7226 (mm-30) REVERT: D 642 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8780 (mt) REVERT: D 689 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: D 712 ARG cc_start: 0.7980 (mtp180) cc_final: 0.7592 (mtm180) outliers start: 96 outliers final: 41 residues processed: 365 average time/residue: 1.0194 time to fit residues: 428.0811 Evaluate side-chains 342 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 288 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 133 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 233 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 107 optimal weight: 0.0060 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19316 Z= 0.155 Angle : 0.522 5.988 26281 Z= 0.272 Chirality : 0.036 0.139 3092 Planarity : 0.004 0.071 3199 Dihedral : 12.166 88.448 2978 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.06 % Allowed : 27.44 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2408 helix: 0.55 (0.13), residues: 1578 sheet: -1.00 (0.62), residues: 64 loop : -2.13 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 380 HIS 0.005 0.001 HIS B 301 PHE 0.010 0.001 PHE C 666 TYR 0.015 0.001 TYR C 451 ARG 0.011 0.001 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 288 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 HIS cc_start: 0.6809 (m-70) cc_final: 0.6609 (m90) REVERT: B 358 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8170 (tttm) REVERT: B 446 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7534 (m) REVERT: B 447 PHE cc_start: 0.8085 (m-80) cc_final: 0.7779 (m-10) REVERT: B 487 ARG cc_start: 0.7649 (mtt90) cc_final: 0.5918 (ttt90) REVERT: B 492 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 516 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7601 (pp) REVERT: B 546 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7291 (tp30) REVERT: B 570 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: B 611 LYS cc_start: 0.7808 (ttmm) cc_final: 0.7585 (ttmt) REVERT: B 631 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 712 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7611 (mtm180) REVERT: B 717 MET cc_start: 0.7391 (mpp) cc_final: 0.6722 (mpp) REVERT: C 288 ASP cc_start: 0.8309 (t0) cc_final: 0.7997 (t0) REVERT: C 378 THR cc_start: 0.8011 (m) cc_final: 0.7620 (m) REVERT: C 483 GLN cc_start: 0.6245 (tm130) cc_final: 0.5697 (tm130) REVERT: C 690 ARG cc_start: 0.7515 (ttm110) cc_final: 0.7093 (ttp-110) REVERT: C 694 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8408 (mp) REVERT: C 702 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: A 213 TYR cc_start: 0.8195 (m-80) cc_final: 0.7851 (m-80) REVERT: A 214 GLU cc_start: 0.7940 (tt0) cc_final: 0.7708 (tt0) REVERT: A 378 THR cc_start: 0.8158 (m) cc_final: 0.7788 (m) REVERT: A 513 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8397 (mt) REVERT: A 687 GLU cc_start: 0.7472 (tp30) cc_final: 0.7205 (tp30) REVERT: A 694 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 702 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6772 (mt-10) REVERT: D 358 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8185 (tttm) REVERT: D 446 CYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7563 (m) REVERT: D 447 PHE cc_start: 0.8102 (m-80) cc_final: 0.7795 (m-10) REVERT: D 492 ILE cc_start: 0.8548 (mp) cc_final: 0.8338 (mp) REVERT: D 516 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7466 (pp) REVERT: D 546 GLU cc_start: 0.6828 (tp30) cc_final: 0.6605 (tp30) REVERT: D 631 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7226 (mm-30) REVERT: D 642 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8780 (mt) REVERT: D 689 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: D 712 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7592 (mtm180) outliers start: 54 outliers final: 41 residues processed: 318 average time/residue: 1.0975 time to fit residues: 399.0191 Evaluate side-chains 341 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19316 Z= 0.155 Angle : 0.522 5.988 26281 Z= 0.272 Chirality : 0.036 0.139 3092 Planarity : 0.004 0.071 3199 Dihedral : 12.166 88.448 2978 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.06 % Allowed : 27.49 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2408 helix: 0.55 (0.13), residues: 1578 sheet: -1.00 (0.62), residues: 64 loop : -2.13 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 380 HIS 0.005 0.001 HIS B 301 PHE 0.010 0.001 PHE C 666 TYR 0.015 0.001 TYR C 451 ARG 0.011 0.001 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 358 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8170 (tttm) REVERT: B 446 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7534 (m) REVERT: B 447 PHE cc_start: 0.8084 (m-80) cc_final: 0.7779 (m-10) REVERT: B 487 ARG cc_start: 0.7649 (mtt90) cc_final: 0.5918 (ttt90) REVERT: B 492 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 516 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7601 (pp) REVERT: B 546 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7291 (tp30) REVERT: B 570 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: B 611 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7585 (ttmt) REVERT: B 631 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 712 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7611 (mtm180) REVERT: B 717 MET cc_start: 0.7391 (mpp) cc_final: 0.6722 (mpp) REVERT: C 288 ASP cc_start: 0.8309 (t0) cc_final: 0.7997 (t0) REVERT: C 378 THR cc_start: 0.8011 (m) cc_final: 0.7620 (m) REVERT: C 483 GLN cc_start: 0.6245 (tm130) cc_final: 0.5697 (tm130) REVERT: C 690 ARG cc_start: 0.7515 (ttm110) cc_final: 0.7093 (ttp-110) REVERT: C 694 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8408 (mp) REVERT: C 702 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: A 213 TYR cc_start: 0.8195 (m-80) cc_final: 0.7851 (m-80) REVERT: A 214 GLU cc_start: 0.7940 (tt0) cc_final: 0.7708 (tt0) REVERT: A 378 THR cc_start: 0.8158 (m) cc_final: 0.7788 (m) REVERT: A 513 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8397 (mt) REVERT: A 687 GLU cc_start: 0.7472 (tp30) cc_final: 0.7205 (tp30) REVERT: A 694 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 702 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6772 (mt-10) REVERT: D 358 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8185 (tttm) REVERT: D 446 CYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7563 (m) REVERT: D 447 PHE cc_start: 0.8102 (m-80) cc_final: 0.7795 (m-10) REVERT: D 492 ILE cc_start: 0.8548 (mp) cc_final: 0.8338 (mp) REVERT: D 516 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7466 (pp) REVERT: D 546 GLU cc_start: 0.6828 (tp30) cc_final: 0.6605 (tp30) REVERT: D 631 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7226 (mm-30) REVERT: D 642 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8780 (mt) REVERT: D 689 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: D 712 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7592 (mtm180) outliers start: 54 outliers final: 41 residues processed: 317 average time/residue: 1.0902 time to fit residues: 395.2625 Evaluate side-chains 341 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 196 optimal weight: 0.0370 chunk 205 optimal weight: 0.7980 chunk 216 optimal weight: 7.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19316 Z= 0.190 Angle : 0.541 6.027 26281 Z= 0.281 Chirality : 0.037 0.150 3092 Planarity : 0.004 0.079 3199 Dihedral : 12.075 89.685 2978 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.80 % Allowed : 26.47 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2408 helix: 0.58 (0.13), residues: 1594 sheet: -0.92 (0.62), residues: 64 loop : -2.25 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 380 HIS 0.014 0.001 HIS D 745 PHE 0.024 0.001 PHE A 489 TYR 0.021 0.001 TYR B 390 ARG 0.014 0.001 ARG B 369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 288 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 358 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8171 (tttm) REVERT: B 446 CYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7556 (m) REVERT: B 447 PHE cc_start: 0.8089 (m-80) cc_final: 0.7784 (m-10) REVERT: B 487 ARG cc_start: 0.7649 (mtt90) cc_final: 0.5919 (ttt90) REVERT: B 492 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8560 (mp) REVERT: B 516 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7575 (pp) REVERT: B 546 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7350 (tp30) REVERT: B 570 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.6366 (pm20) REVERT: B 611 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7623 (ttmt) REVERT: B 631 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 712 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7615 (mtm180) REVERT: B 717 MET cc_start: 0.7388 (mpp) cc_final: 0.6740 (mpp) REVERT: C 288 ASP cc_start: 0.8312 (t0) cc_final: 0.7998 (t0) REVERT: C 378 THR cc_start: 0.8016 (m) cc_final: 0.7626 (m) REVERT: C 483 GLN cc_start: 0.6242 (tm130) cc_final: 0.5691 (tm130) REVERT: C 690 ARG cc_start: 0.7497 (ttm110) cc_final: 0.7102 (ttp-110) REVERT: C 694 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8430 (mp) REVERT: C 702 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: A 213 TYR cc_start: 0.8218 (m-80) cc_final: 0.7889 (m-80) REVERT: A 378 THR cc_start: 0.8168 (m) cc_final: 0.7801 (m) REVERT: A 513 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 687 GLU cc_start: 0.7472 (tp30) cc_final: 0.7214 (tp30) REVERT: A 694 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8486 (mp) REVERT: A 702 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: D 358 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8186 (tttm) REVERT: D 446 CYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7490 (m) REVERT: D 447 PHE cc_start: 0.8106 (m-80) cc_final: 0.7801 (m-10) REVERT: D 492 ILE cc_start: 0.8519 (mp) cc_final: 0.8283 (mp) REVERT: D 516 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7456 (pp) REVERT: D 546 GLU cc_start: 0.6782 (tp30) cc_final: 0.6523 (tp30) REVERT: D 631 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7237 (mm-30) REVERT: D 642 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8777 (mt) REVERT: D 689 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: D 712 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7595 (mtm180) outliers start: 67 outliers final: 41 residues processed: 325 average time/residue: 1.0950 time to fit residues: 406.8805 Evaluate side-chains 345 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 291 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 221 optimal weight: 0.0370 chunk 191 optimal weight: 0.9980 chunk 19 optimal weight: 0.0370 chunk 148 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19316 Z= 0.190 Angle : 0.541 6.027 26281 Z= 0.281 Chirality : 0.037 0.150 3092 Planarity : 0.004 0.079 3199 Dihedral : 12.075 89.685 2978 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.06 % Allowed : 27.55 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2408 helix: 0.58 (0.13), residues: 1594 sheet: -0.92 (0.62), residues: 64 loop : -2.25 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 380 HIS 0.014 0.001 HIS D 745 PHE 0.024 0.001 PHE A 489 TYR 0.021 0.001 TYR B 390 ARG 0.014 0.001 ARG B 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 291 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 358 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8171 (tttm) REVERT: B 446 CYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7557 (m) REVERT: B 447 PHE cc_start: 0.8088 (m-80) cc_final: 0.7784 (m-10) REVERT: B 487 ARG cc_start: 0.7647 (mtt90) cc_final: 0.5919 (ttt90) REVERT: B 492 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8560 (mp) REVERT: B 516 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7575 (pp) REVERT: B 546 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7350 (tp30) REVERT: B 570 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6366 (pm20) REVERT: B 611 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7623 (ttmt) REVERT: B 631 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 712 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7615 (mtm180) REVERT: B 717 MET cc_start: 0.7388 (mpp) cc_final: 0.6740 (mpp) REVERT: C 288 ASP cc_start: 0.8312 (t0) cc_final: 0.7999 (t0) REVERT: C 378 THR cc_start: 0.8018 (m) cc_final: 0.7627 (m) REVERT: C 483 GLN cc_start: 0.6247 (tm130) cc_final: 0.5692 (tm130) REVERT: C 690 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7102 (ttp-110) REVERT: C 694 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 702 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: A 213 TYR cc_start: 0.8220 (m-80) cc_final: 0.7889 (m-80) REVERT: A 378 THR cc_start: 0.8169 (m) cc_final: 0.7801 (m) REVERT: A 513 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 687 GLU cc_start: 0.7471 (tp30) cc_final: 0.7214 (tp30) REVERT: A 694 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8486 (mp) REVERT: A 702 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: D 358 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8186 (tttm) REVERT: D 446 CYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7490 (m) REVERT: D 447 PHE cc_start: 0.8105 (m-80) cc_final: 0.7801 (m-10) REVERT: D 492 ILE cc_start: 0.8519 (mp) cc_final: 0.8283 (mp) REVERT: D 516 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7456 (pp) REVERT: D 546 GLU cc_start: 0.6745 (tp30) cc_final: 0.6523 (tp30) REVERT: D 631 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7237 (mm-30) REVERT: D 642 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8777 (mt) REVERT: D 689 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: D 712 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7595 (mtm180) outliers start: 54 outliers final: 41 residues processed: 321 average time/residue: 1.1139 time to fit residues: 411.6802 Evaluate side-chains 343 residues out of total 2166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 289 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 177 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 192 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 35 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN C 284 HIS ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119099 restraints weight = 23123.169| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.95 r_work: 0.3182 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19316 Z= 0.162 Angle : 0.534 8.373 26281 Z= 0.277 Chirality : 0.036 0.210 3092 Planarity : 0.004 0.074 3199 Dihedral : 12.007 88.543 2978 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.40 % Allowed : 27.10 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2408 helix: 0.66 (0.13), residues: 1590 sheet: -0.90 (0.62), residues: 64 loop : -2.19 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 380 HIS 0.010 0.001 HIS D 745 PHE 0.013 0.001 PHE A 489 TYR 0.016 0.001 TYR B 390 ARG 0.012 0.001 ARG B 690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7046.72 seconds wall clock time: 125 minutes 20.32 seconds (7520.32 seconds total)