Starting phenix.real_space_refine on Sat Feb 17 10:50:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj2_33217/02_2024/7xj2_33217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj2_33217/02_2024/7xj2_33217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj2_33217/02_2024/7xj2_33217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj2_33217/02_2024/7xj2_33217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj2_33217/02_2024/7xj2_33217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj2_33217/02_2024/7xj2_33217_updated.pdb" } resolution = 3.64 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= 0.005 sd= 0.068 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 112 5.16 5 C 12123 2.51 5 N 3074 2.21 5 O 3117 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" 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 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B ASP 752": "OD1" <-> "OD2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "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 "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ASP 240": "OD1" <-> "OD2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D ASP 293": "OD1" <-> "OD2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 569": "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 TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 687": "OE1" <-> "OE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18438 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4585 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 27, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 248 Chain: "C" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4575 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 258 Chain: "A" Number of atoms: 4571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4571 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 262 Chain: "D" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4575 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 258 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'EQK': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'EQK': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'EQK': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'EQK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.30, per 1000 atoms: 0.56 Number of scatterers: 18438 At special positions: 0 Unit cell: (117.52, 117.52, 123.76, 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 112 16.00 F 12 9.00 O 3117 8.00 N 3074 7.00 C 12123 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: 7.52 Conformation dependent library (CDL) restraints added in 3.4 seconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 60.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 134 through 148 Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 183 through 196 removed outlier: 4.154A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (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 236 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 305 Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 332 through 335 No H-bonds generated for 'chain 'B' and resid 332 through 335' 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 421 removed outlier: 5.151A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 460 removed outlier: 4.258A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N HIS B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 507 removed outlier: 4.258A pdb=" N LEU B 507 " --> pdb=" O ILE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 541 Processing helix chain 'B' and resid 547 through 567 removed outlier: 4.541A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 587 through 608 Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 651 through 678 Processing helix chain 'B' and resid 680 through 706 removed outlier: 5.066A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 715 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 134 through 148 Processing helix chain 'C' and resid 155 through 162 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 183 through 196 removed outlier: 4.101A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (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 305 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 332 through 335 No H-bonds generated for 'chain 'C' and resid 332 through 335' Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 368 through 373 removed outlier: 5.463A pdb=" N SER C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 416 through 421 removed outlier: 5.045A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 460 removed outlier: 4.249A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N HIS C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 507 removed outlier: 4.187A pdb=" N LEU C 507 " --> pdb=" O ILE C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 541 Processing helix chain 'C' and resid 548 through 566 removed outlier: 5.017A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 608 removed outlier: 4.222A pdb=" N VAL C 587 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 651 through 677 Processing helix chain 'C' and resid 680 through 706 removed outlier: 5.256A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 183 through 196 removed outlier: 4.149A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (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 305 Processing helix chain 'A' and resid 310 through 313 No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 332 through 335 No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 368 through 373 removed outlier: 5.438A pdb=" N SER A 372 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 416 through 421 removed outlier: 5.117A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 460 removed outlier: 4.255A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 507 removed outlier: 4.292A pdb=" N LEU A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 541 Processing helix chain 'A' and resid 547 through 565 removed outlier: 5.386A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 651 through 677 Processing helix chain 'A' and resid 680 through 706 removed outlier: 5.118A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.539A 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 134 through 148 Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 183 through 196 removed outlier: 4.120A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (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 236 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 305 Processing helix chain 'D' and resid 310 through 313 No H-bonds generated for 'chain 'D' and resid 310 through 313' Processing helix chain 'D' and resid 317 through 327 Processing helix chain 'D' and resid 332 through 335 No H-bonds generated for 'chain 'D' and resid 332 through 335' Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.513A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 409 Processing helix chain 'D' and resid 416 through 421 removed outlier: 5.102A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 460 removed outlier: 4.255A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 505 removed outlier: 4.059A pdb=" N GLY D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 541 Processing helix chain 'D' and resid 547 through 564 removed outlier: 5.044A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 608 removed outlier: 3.920A pdb=" N VAL D 587 " --> pdb=" O ILE D 583 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (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 680 through 706 removed outlier: 5.137A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) 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 376 through 378 Processing sheet with id= C, first strand: chain 'A' and resid 376 through 378 Processing sheet with id= D, first strand: chain 'D' and resid 376 through 378 990 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.48: 10625 1.48 - 1.84: 8212 1.84 - 2.19: 0 2.19 - 2.54: 0 2.54 - 2.89: 2 Bond restraints: 18839 Sorted by residual: bond pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 1.332 2.895 -1.562 1.40e-02 5.10e+03 1.25e+04 bond pdb=" C PRO C 613 " pdb=" N ASN C 616 " ideal model delta sigma weight residual 1.334 2.894 -1.560 1.42e-02 4.96e+03 1.21e+04 bond pdb=" C20 EQK D1101 " pdb=" S01 EQK D1101 " ideal model delta sigma weight residual 1.732 1.509 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C20 EQK B1101 " pdb=" S01 EQK B1101 " ideal model delta sigma weight residual 1.732 1.511 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C20 EQK C1101 " pdb=" S01 EQK C1101 " ideal model delta sigma weight residual 1.732 1.511 0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 18834 not shown) Histogram of bond angle deviations from ideal: 73.44 - 94.75: 2 94.75 - 116.06: 12176 116.06 - 137.37: 13476 137.37 - 158.67: 2 158.67 - 179.98: 4 Bond angle restraints: 25660 Sorted by residual: angle pdb=" O PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 122.64 73.44 49.20 1.35e+00 5.49e-01 1.33e+03 angle pdb=" O PRO C 613 " pdb=" C PRO C 613 " pdb=" N ASN C 616 " ideal model delta sigma weight residual 122.64 74.81 47.83 1.35e+00 5.49e-01 1.26e+03 angle pdb=" C PRO C 613 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta sigma weight residual 122.36 146.31 -23.95 1.47e+00 4.63e-01 2.65e+02 angle pdb=" C PRO B 613 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 121.54 145.84 -24.30 1.91e+00 2.74e-01 1.62e+02 angle pdb=" CA PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 116.70 133.32 -16.62 2.07e+00 2.33e-01 6.45e+01 ... (remaining 25655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 10353 24.87 - 49.74: 561 49.74 - 74.61: 81 74.61 - 99.49: 39 99.49 - 124.36: 2 Dihedral angle restraints: 11036 sinusoidal: 3899 harmonic: 7137 Sorted by residual: dihedral pdb=" CA PRO C 613 " pdb=" C PRO C 613 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta harmonic sigma weight residual -180.00 -55.64 -124.36 0 5.00e+00 4.00e-02 6.19e+02 dihedral pdb=" CA PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta harmonic sigma weight residual -180.00 -59.93 -120.07 0 5.00e+00 4.00e-02 5.77e+02 dihedral pdb=" CA HIS C 585 " pdb=" C HIS C 585 " pdb=" N ASP C 586 " pdb=" CA ASP C 586 " ideal model delta harmonic sigma weight residual 180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 11033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2848 0.074 - 0.147: 208 0.147 - 0.221: 7 0.221 - 0.295: 0 0.295 - 0.368: 1 Chirality restraints: 3064 Sorted by residual: chirality pdb=" CA GLU A 702 " pdb=" N GLU A 702 " pdb=" C GLU A 702 " pdb=" CB GLU A 702 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA ARG D 462 " pdb=" N ARG D 462 " pdb=" C ARG D 462 " pdb=" CB ARG D 462 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 704 " pdb=" N GLU A 704 " pdb=" C GLU A 704 " pdb=" CB GLU A 704 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3061 not shown) Planarity restraints: 3145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 613 " 0.176 2.00e-02 2.50e+03 2.19e-01 4.80e+02 pdb=" C PRO C 613 " -0.372 2.00e-02 2.50e+03 pdb=" O PRO C 613 " 0.139 2.00e-02 2.50e+03 pdb=" N ASN C 616 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 613 " -0.176 2.00e-02 2.50e+03 2.18e-01 4.76e+02 pdb=" C PRO B 613 " 0.370 2.00e-02 2.50e+03 pdb=" O PRO B 613 " -0.138 2.00e-02 2.50e+03 pdb=" N ASN B 616 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 566 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C THR D 566 " -0.033 2.00e-02 2.50e+03 pdb=" O THR D 566 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG D 567 " 0.011 2.00e-02 2.50e+03 ... (remaining 3142 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2120 2.74 - 3.28: 20118 3.28 - 3.82: 31007 3.82 - 4.36: 35685 4.36 - 4.90: 60060 Nonbonded interactions: 148990 Sorted by model distance: nonbonded pdb=" OH TYR A 260 " pdb=" ND2 ASN A 297 " model vdw 2.203 2.520 nonbonded pdb=" OG SER A 620 " pdb=" CA GLN A 646 " model vdw 2.213 3.470 nonbonded pdb=" OG1 THR D 636 " pdb=" OH TYR D 661 " model vdw 2.223 2.440 nonbonded pdb=" OE2 GLU C 334 " pdb=" NH2 ARG C 363 " model vdw 2.225 2.520 nonbonded pdb=" OG1 THR C 636 " pdb=" OH TYR C 661 " model vdw 2.226 2.440 ... (remaining 148985 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 749 or (resid 750 through 752 and (name N or n \ ame CA or name C or name O or name CB )) or resid 753 through 754 or resid 1101) \ ) selection = (chain 'B' and (resid 118 through 621 or (resid 622 and (name N or name CA or na \ me C or name O or name CB )) or resid 623 through 749 or (resid 750 through 752 \ and (name N or name CA or name C or name O or name CB )) or resid 753 through 75 \ 4 or resid 1101)) selection = (chain 'C' and (resid 118 through 621 or (resid 622 and (name N or name CA or na \ me C or name O or name CB )) or resid 623 through 754 or resid 1101)) selection = (chain 'D' and (resid 118 through 621 or (resid 622 and (name N or name CA or na \ me C or name O or name CB )) or resid 623 through 754 or resid 1101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.000 Extract box with map and model: 4.180 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 51.490 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.120 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:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.019 1.562 18839 Z= 0.883 Angle : 0.903 49.198 25660 Z= 0.536 Chirality : 0.040 0.368 3064 Planarity : 0.006 0.219 3145 Dihedral : 16.461 124.358 6396 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.75 % Allowed : 18.44 % Favored : 77.81 % 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: -3.17 (0.15), residues: 2388 helix: -1.29 (0.11), residues: 1524 sheet: -5.07 (0.32), residues: 84 loop : -3.21 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 380 HIS 0.003 0.001 HIS D 301 PHE 0.012 0.001 PHE D 601 TYR 0.020 0.002 TYR B 451 ARG 0.003 0.000 ARG D 696 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 480 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 GLN cc_start: 0.8622 (mt0) cc_final: 0.8414 (mt0) REVERT: B 318 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8604 (ttpt) REVERT: B 528 ILE cc_start: 0.9306 (mt) cc_final: 0.9014 (mm) REVERT: B 594 TYR cc_start: 0.8444 (t80) cc_final: 0.8209 (t80) REVERT: C 318 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8647 (ttpt) REVERT: C 555 MET cc_start: 0.8620 (tmm) cc_final: 0.8344 (tmm) REVERT: C 559 TRP cc_start: 0.8673 (m100) cc_final: 0.8209 (m100) REVERT: C 594 TYR cc_start: 0.8428 (t80) cc_final: 0.8044 (t80) REVERT: A 227 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8247 (mm110) REVERT: A 318 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8654 (ttpt) REVERT: A 528 ILE cc_start: 0.9293 (mt) cc_final: 0.8976 (mm) REVERT: A 555 MET cc_start: 0.8403 (tmm) cc_final: 0.8185 (tmm) REVERT: A 573 SER cc_start: 0.8411 (t) cc_final: 0.7805 (m) REVERT: A 591 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8436 (mm) REVERT: A 611 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.4726 (mptt) REVERT: A 690 ARG cc_start: 0.7918 (ptm-80) cc_final: 0.7482 (mtp-110) REVERT: A 712 ARG cc_start: 0.9060 (mtp180) cc_final: 0.8773 (mtm-85) REVERT: D 318 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8638 (ttpt) REVERT: D 569 PHE cc_start: 0.5991 (m-80) cc_final: 0.5735 (t80) REVERT: D 573 SER cc_start: 0.8327 (t) cc_final: 0.7697 (m) REVERT: D 594 TYR cc_start: 0.8489 (t80) cc_final: 0.8104 (t80) REVERT: D 611 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.5826 (mptt) REVERT: D 745 HIS cc_start: 0.7496 (m-70) cc_final: 0.7290 (m170) outliers start: 65 outliers final: 35 residues processed: 528 average time/residue: 0.3120 time to fit residues: 245.0095 Evaluate side-chains 409 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 371 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 0.4980 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN B 279 GLN B 284 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 346 GLN B 452 ASN B 647 ASN C 178 ASN C 284 HIS ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN C 346 GLN C 452 ASN C 570 GLN A 284 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 346 GLN A 452 ASN A 570 GLN A 745 HIS D 205 ASN D 284 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN D 346 GLN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18839 Z= 0.252 Angle : 0.596 8.473 25660 Z= 0.304 Chirality : 0.038 0.141 3064 Planarity : 0.004 0.042 3145 Dihedral : 11.569 88.975 2764 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.56 % Rotamer: Outliers : 4.32 % Allowed : 24.50 % Favored : 71.18 % 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: -1.42 (0.17), residues: 2392 helix: 0.13 (0.13), residues: 1508 sheet: -4.16 (0.41), residues: 64 loop : -2.68 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 380 HIS 0.005 0.001 HIS A 745 PHE 0.012 0.001 PHE C 193 TYR 0.016 0.001 TYR C 451 ARG 0.004 0.000 ARG C 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 391 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8614 (ttpt) REVERT: B 528 ILE cc_start: 0.9185 (mt) cc_final: 0.8963 (mm) REVERT: B 594 TYR cc_start: 0.8550 (t80) cc_final: 0.8281 (t80) REVERT: B 635 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8683 (tt) REVERT: C 318 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8641 (ttpt) REVERT: C 419 MET cc_start: 0.8394 (mtp) cc_final: 0.8184 (ttm) REVERT: C 452 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7480 (t0) REVERT: C 594 TYR cc_start: 0.8429 (t80) cc_final: 0.8111 (t80) REVERT: A 318 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8635 (ttpt) REVERT: A 578 MET cc_start: 0.8043 (ptt) cc_final: 0.7774 (ptt) REVERT: D 318 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8631 (ttpt) REVERT: D 573 SER cc_start: 0.8293 (t) cc_final: 0.7665 (m) REVERT: D 591 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8323 (mm) REVERT: D 627 ASP cc_start: 0.8115 (m-30) cc_final: 0.7714 (m-30) REVERT: D 634 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8627 (mtpp) outliers start: 75 outliers final: 51 residues processed: 444 average time/residue: 0.2863 time to fit residues: 199.1749 Evaluate side-chains 429 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 375 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.0570 chunk 67 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 0.0970 chunk 60 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18839 Z= 0.200 Angle : 0.556 7.544 25660 Z= 0.284 Chirality : 0.037 0.165 3064 Planarity : 0.003 0.042 3145 Dihedral : 11.356 89.428 2726 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 5.07 % Allowed : 24.96 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2392 helix: 0.77 (0.13), residues: 1504 sheet: -3.59 (0.47), residues: 64 loop : -2.42 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 380 HIS 0.010 0.001 HIS D 160 PHE 0.008 0.001 PHE A 601 TYR 0.017 0.001 TYR C 451 ARG 0.003 0.000 ARG C 698 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 406 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8580 (ttpt) REVERT: B 419 MET cc_start: 0.8467 (ttm) cc_final: 0.8237 (ttm) REVERT: B 541 LEU cc_start: 0.8572 (mm) cc_final: 0.8259 (tt) REVERT: B 559 TRP cc_start: 0.8896 (m100) cc_final: 0.8578 (m100) REVERT: B 578 MET cc_start: 0.8128 (ptt) cc_final: 0.7876 (ptt) REVERT: C 318 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8616 (ttpt) REVERT: C 419 MET cc_start: 0.8351 (mtp) cc_final: 0.8074 (ttm) REVERT: C 452 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7430 (t0) REVERT: C 460 TYR cc_start: 0.8089 (t80) cc_final: 0.7822 (t80) REVERT: C 599 LEU cc_start: 0.8751 (mm) cc_final: 0.7924 (tt) REVERT: A 193 PHE cc_start: 0.7591 (t80) cc_final: 0.7379 (t80) REVERT: A 318 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8605 (ttpt) REVERT: A 419 MET cc_start: 0.8457 (ttm) cc_final: 0.8236 (ttm) REVERT: A 689 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8318 (mp0) REVERT: D 318 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8657 (ttpt) REVERT: D 419 MET cc_start: 0.8428 (ttm) cc_final: 0.8227 (ttm) REVERT: D 521 TRP cc_start: 0.8692 (m-10) cc_final: 0.7750 (m100) REVERT: D 562 MET cc_start: 0.8561 (tpp) cc_final: 0.8289 (tpp) REVERT: D 573 SER cc_start: 0.8225 (t) cc_final: 0.7615 (m) REVERT: D 591 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8314 (mm) REVERT: D 594 TYR cc_start: 0.8561 (t80) cc_final: 0.8286 (t80) REVERT: D 690 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7860 (mtp-110) outliers start: 88 outliers final: 55 residues processed: 467 average time/residue: 0.2729 time to fit residues: 198.1040 Evaluate side-chains 437 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 380 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 0.0570 chunk 231 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18839 Z= 0.175 Angle : 0.543 7.166 25660 Z= 0.277 Chirality : 0.037 0.155 3064 Planarity : 0.003 0.042 3145 Dihedral : 11.201 89.892 2720 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 4.73 % Allowed : 25.65 % Favored : 69.63 % 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: -0.22 (0.18), residues: 2392 helix: 1.10 (0.13), residues: 1504 sheet: -3.21 (0.50), residues: 64 loop : -2.29 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 380 HIS 0.004 0.001 HIS B 745 PHE 0.010 0.001 PHE B 527 TYR 0.013 0.001 TYR C 451 ARG 0.003 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 404 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8593 (ttpt) REVERT: B 419 MET cc_start: 0.8474 (ttm) cc_final: 0.8249 (ttm) REVERT: B 559 TRP cc_start: 0.8872 (m100) cc_final: 0.8504 (m100) REVERT: C 318 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8631 (ttpt) REVERT: C 419 MET cc_start: 0.8342 (mtp) cc_final: 0.8141 (ttm) REVERT: C 452 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7518 (t0) REVERT: C 460 TYR cc_start: 0.8102 (t80) cc_final: 0.7833 (t80) REVERT: C 545 LYS cc_start: 0.7003 (mmtt) cc_final: 0.6294 (mmtt) REVERT: C 599 LEU cc_start: 0.8693 (mm) cc_final: 0.7942 (tt) REVERT: A 318 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8607 (ttpt) REVERT: A 419 MET cc_start: 0.8445 (ttm) cc_final: 0.8238 (ttm) REVERT: A 569 PHE cc_start: 0.5705 (m-80) cc_final: 0.5399 (t80) REVERT: A 580 GLN cc_start: 0.8495 (tt0) cc_final: 0.8098 (tt0) REVERT: A 690 ARG cc_start: 0.8237 (ptp90) cc_final: 0.7772 (ptm160) REVERT: D 156 ASP cc_start: 0.8523 (t0) cc_final: 0.8098 (t0) REVERT: D 318 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8648 (ttpt) REVERT: D 419 MET cc_start: 0.8476 (ttm) cc_final: 0.8271 (ttm) REVERT: D 452 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7545 (t0) REVERT: D 573 SER cc_start: 0.8231 (t) cc_final: 0.7581 (m) REVERT: D 591 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8310 (mm) REVERT: D 594 TYR cc_start: 0.8561 (t80) cc_final: 0.8338 (t80) outliers start: 82 outliers final: 60 residues processed: 455 average time/residue: 0.2726 time to fit residues: 194.1758 Evaluate side-chains 437 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 374 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 690 ARG Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18839 Z= 0.190 Angle : 0.570 9.427 25660 Z= 0.288 Chirality : 0.038 0.166 3064 Planarity : 0.003 0.041 3145 Dihedral : 11.108 89.539 2713 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 5.59 % Allowed : 25.88 % Favored : 68.53 % 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: -0.07 (0.18), residues: 2392 helix: 1.22 (0.13), residues: 1508 sheet: -3.15 (0.48), residues: 64 loop : -2.25 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 380 HIS 0.004 0.001 HIS D 160 PHE 0.011 0.001 PHE D 157 TYR 0.021 0.001 TYR C 594 ARG 0.003 0.000 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 391 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8591 (ttpt) REVERT: B 419 MET cc_start: 0.8457 (ttm) cc_final: 0.8240 (ttm) REVERT: B 431 MET cc_start: 0.7866 (ttt) cc_final: 0.7476 (ttt) REVERT: B 487 ARG cc_start: 0.4885 (mtt90) cc_final: 0.3268 (mtp180) REVERT: B 541 LEU cc_start: 0.8529 (mm) cc_final: 0.8257 (tt) REVERT: B 559 TRP cc_start: 0.8861 (m100) cc_final: 0.8461 (m100) REVERT: C 318 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8633 (ttpt) REVERT: C 339 ASN cc_start: 0.8478 (m110) cc_final: 0.8168 (m-40) REVERT: C 431 MET cc_start: 0.7875 (ttt) cc_final: 0.7537 (ttt) REVERT: C 460 TYR cc_start: 0.8120 (t80) cc_final: 0.7866 (t80) REVERT: C 545 LYS cc_start: 0.7014 (mmtt) cc_final: 0.6367 (mmtt) REVERT: C 599 LEU cc_start: 0.8670 (mm) cc_final: 0.7930 (tt) REVERT: A 268 LEU cc_start: 0.9380 (tp) cc_final: 0.9106 (tp) REVERT: A 318 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8633 (ttpt) REVERT: A 419 MET cc_start: 0.8437 (ttm) cc_final: 0.8230 (ttm) REVERT: A 431 MET cc_start: 0.7866 (ttt) cc_final: 0.7531 (ttt) REVERT: A 580 GLN cc_start: 0.8542 (tt0) cc_final: 0.8132 (tt0) REVERT: A 690 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7723 (ptm160) REVERT: D 318 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8660 (ttpt) REVERT: D 573 SER cc_start: 0.8252 (t) cc_final: 0.7594 (m) REVERT: D 587 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8755 (p) REVERT: D 591 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8313 (mm) outliers start: 97 outliers final: 70 residues processed: 451 average time/residue: 0.2924 time to fit residues: 208.9020 Evaluate side-chains 452 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 380 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 690 ARG Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 694 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 136 optimal weight: 0.0060 chunk 57 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 0.0040 chunk 19 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 0.0270 overall best weight: 0.2866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 452 ASN C 483 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18839 Z= 0.140 Angle : 0.552 11.516 25660 Z= 0.276 Chirality : 0.037 0.174 3064 Planarity : 0.003 0.040 3145 Dihedral : 11.034 89.238 2713 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 4.44 % Allowed : 27.32 % Favored : 68.24 % 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: 0.20 (0.18), residues: 2392 helix: 1.44 (0.13), residues: 1504 sheet: -3.05 (0.47), residues: 64 loop : -2.16 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 380 HIS 0.017 0.001 HIS D 160 PHE 0.010 0.001 PHE C 193 TYR 0.021 0.001 TYR D 594 ARG 0.003 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 401 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 PHE cc_start: 0.7472 (t80) cc_final: 0.7239 (t80) REVERT: B 318 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8548 (ttpt) REVERT: B 419 MET cc_start: 0.8470 (ttm) cc_final: 0.8266 (ttm) REVERT: B 487 ARG cc_start: 0.4760 (mtt90) cc_final: 0.3150 (mtp180) REVERT: B 541 LEU cc_start: 0.8504 (mm) cc_final: 0.8228 (tt) REVERT: B 559 TRP cc_start: 0.8831 (m100) cc_final: 0.8426 (m100) REVERT: C 268 LEU cc_start: 0.9278 (tp) cc_final: 0.9013 (tp) REVERT: C 318 LYS cc_start: 0.8884 (ttmt) cc_final: 0.8596 (ttpt) REVERT: C 460 TYR cc_start: 0.8098 (t80) cc_final: 0.7871 (t80) REVERT: C 521 TRP cc_start: 0.8754 (m-10) cc_final: 0.8534 (m-10) REVERT: C 545 LYS cc_start: 0.7000 (mmtt) cc_final: 0.6380 (mmpt) REVERT: C 580 GLN cc_start: 0.8431 (tt0) cc_final: 0.8227 (tt0) REVERT: C 599 LEU cc_start: 0.8568 (mm) cc_final: 0.7905 (tt) REVERT: A 268 LEU cc_start: 0.9335 (tp) cc_final: 0.9029 (tp) REVERT: A 318 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8598 (ttpt) REVERT: A 580 GLN cc_start: 0.8546 (tt0) cc_final: 0.8151 (tt0) REVERT: A 690 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7715 (ptm160) REVERT: D 156 ASP cc_start: 0.8393 (t0) cc_final: 0.8120 (t0) REVERT: D 318 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8619 (ttpt) REVERT: D 521 TRP cc_start: 0.8659 (m-10) cc_final: 0.7577 (m100) REVERT: D 573 SER cc_start: 0.8013 (t) cc_final: 0.7430 (m) REVERT: D 591 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8346 (mm) outliers start: 77 outliers final: 54 residues processed: 446 average time/residue: 0.2649 time to fit residues: 185.9382 Evaluate side-chains 423 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 368 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 694 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 0.0060 chunk 129 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18839 Z= 0.166 Angle : 0.561 9.170 25660 Z= 0.280 Chirality : 0.037 0.179 3064 Planarity : 0.003 0.037 3145 Dihedral : 10.863 89.138 2709 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 4.55 % Allowed : 27.15 % Favored : 68.30 % 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: 0.31 (0.18), residues: 2392 helix: 1.52 (0.13), residues: 1504 sheet: -3.06 (0.46), residues: 64 loop : -2.09 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 380 HIS 0.017 0.001 HIS D 160 PHE 0.010 0.001 PHE D 157 TYR 0.030 0.001 TYR A 594 ARG 0.003 0.000 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 383 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8618 (ttpt) REVERT: B 487 ARG cc_start: 0.4789 (mtt90) cc_final: 0.3116 (mtp180) REVERT: B 541 LEU cc_start: 0.8507 (mm) cc_final: 0.8229 (tt) REVERT: C 268 LEU cc_start: 0.9240 (tp) cc_final: 0.8979 (tp) REVERT: C 318 LYS cc_start: 0.8895 (ttmt) cc_final: 0.8618 (ttpt) REVERT: C 545 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6327 (mmpt) REVERT: C 599 LEU cc_start: 0.8627 (mm) cc_final: 0.7889 (tt) REVERT: A 268 LEU cc_start: 0.9330 (tp) cc_final: 0.8997 (tp) REVERT: A 318 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8613 (ttpt) REVERT: A 371 ARG cc_start: 0.8445 (mtp-110) cc_final: 0.8175 (ttp-110) REVERT: A 580 GLN cc_start: 0.8566 (tt0) cc_final: 0.8157 (tt0) REVERT: D 318 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8624 (ttpt) REVERT: D 573 SER cc_start: 0.8067 (t) cc_final: 0.7414 (m) REVERT: D 587 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8741 (p) REVERT: D 591 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8389 (mm) REVERT: D 671 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8019 (t0) outliers start: 79 outliers final: 59 residues processed: 432 average time/residue: 0.2775 time to fit residues: 187.7725 Evaluate side-chains 426 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 364 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 694 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 181 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18839 Z= 0.158 Angle : 0.583 10.837 25660 Z= 0.289 Chirality : 0.037 0.194 3064 Planarity : 0.003 0.036 3145 Dihedral : 10.794 89.901 2708 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.50 % Allowed : 27.32 % Favored : 68.18 % 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: 0.38 (0.18), residues: 2392 helix: 1.56 (0.13), residues: 1508 sheet: -3.03 (0.46), residues: 64 loop : -2.04 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 380 HIS 0.019 0.001 HIS A 160 PHE 0.012 0.001 PHE D 157 TYR 0.013 0.001 TYR D 594 ARG 0.004 0.000 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 376 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8601 (ttpt) REVERT: B 487 ARG cc_start: 0.4794 (mtt90) cc_final: 0.3192 (mtp180) REVERT: B 541 LEU cc_start: 0.8499 (mm) cc_final: 0.8221 (tt) REVERT: C 268 LEU cc_start: 0.9232 (tp) cc_final: 0.8976 (tp) REVERT: C 318 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8597 (ttpt) REVERT: C 545 LYS cc_start: 0.6948 (mmtt) cc_final: 0.6346 (mmpt) REVERT: C 599 LEU cc_start: 0.8578 (mm) cc_final: 0.7903 (tt) REVERT: A 193 PHE cc_start: 0.7566 (t80) cc_final: 0.7302 (t80) REVERT: A 268 LEU cc_start: 0.9331 (tp) cc_final: 0.8985 (tp) REVERT: A 318 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8626 (ttpt) REVERT: A 371 ARG cc_start: 0.8436 (mtp-110) cc_final: 0.8172 (ttp-110) REVERT: A 580 GLN cc_start: 0.8567 (tt0) cc_final: 0.8156 (tt0) REVERT: A 690 ARG cc_start: 0.8054 (ptp90) cc_final: 0.7704 (ptm160) REVERT: D 318 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8632 (ttpt) REVERT: D 521 TRP cc_start: 0.8565 (m-10) cc_final: 0.7564 (m100) REVERT: D 591 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8390 (mm) REVERT: D 671 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8140 (t0) outliers start: 78 outliers final: 61 residues processed: 425 average time/residue: 0.2765 time to fit residues: 183.0487 Evaluate side-chains 430 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 367 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 694 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 66 optimal weight: 0.0770 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18839 Z= 0.171 Angle : 0.604 14.714 25660 Z= 0.298 Chirality : 0.038 0.267 3064 Planarity : 0.003 0.037 3145 Dihedral : 10.766 89.752 2707 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.03 % Allowed : 28.18 % Favored : 67.78 % 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: 0.43 (0.18), residues: 2392 helix: 1.61 (0.13), residues: 1504 sheet: -3.01 (0.45), residues: 64 loop : -2.02 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 380 HIS 0.017 0.001 HIS D 160 PHE 0.016 0.001 PHE D 157 TYR 0.029 0.001 TYR C 594 ARG 0.006 0.000 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 373 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 193 PHE cc_start: 0.7643 (t80) cc_final: 0.7404 (t80) REVERT: B 318 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8600 (ttpt) REVERT: B 487 ARG cc_start: 0.4775 (mtt90) cc_final: 0.3187 (mtp180) REVERT: B 541 LEU cc_start: 0.8501 (mm) cc_final: 0.8219 (tt) REVERT: C 268 LEU cc_start: 0.9238 (tp) cc_final: 0.8978 (tp) REVERT: C 318 LYS cc_start: 0.8884 (ttmt) cc_final: 0.8603 (ttpt) REVERT: C 545 LYS cc_start: 0.6948 (mmtt) cc_final: 0.6346 (mmpt) REVERT: C 580 GLN cc_start: 0.8493 (tt0) cc_final: 0.8058 (tt0) REVERT: C 599 LEU cc_start: 0.8594 (mm) cc_final: 0.7895 (tt) REVERT: A 193 PHE cc_start: 0.7575 (t80) cc_final: 0.7328 (t80) REVERT: A 268 LEU cc_start: 0.9328 (tp) cc_final: 0.8985 (tp) REVERT: A 318 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8624 (ttpt) REVERT: A 371 ARG cc_start: 0.8441 (mtp-110) cc_final: 0.8179 (ttp-110) REVERT: A 580 GLN cc_start: 0.8572 (tt0) cc_final: 0.8155 (tt0) REVERT: A 690 ARG cc_start: 0.8037 (ptp90) cc_final: 0.7706 (ptm160) REVERT: D 318 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8632 (ttpt) REVERT: D 521 TRP cc_start: 0.8651 (m-10) cc_final: 0.7569 (m100) REVERT: D 591 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8420 (mm) outliers start: 70 outliers final: 63 residues processed: 415 average time/residue: 0.2913 time to fit residues: 188.8414 Evaluate side-chains 428 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 364 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 694 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18839 Z= 0.171 Angle : 0.604 14.714 25660 Z= 0.298 Chirality : 0.038 0.267 3064 Planarity : 0.003 0.037 3145 Dihedral : 10.756 89.752 2706 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.69 % Allowed : 28.76 % Favored : 67.55 % 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: 0.43 (0.18), residues: 2392 helix: 1.61 (0.13), residues: 1504 sheet: -3.01 (0.45), residues: 64 loop : -2.02 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 380 HIS 0.017 0.001 HIS D 160 PHE 0.016 0.001 PHE D 157 TYR 0.029 0.001 TYR C 594 ARG 0.006 0.000 ARG D 690 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 364 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 193 PHE cc_start: 0.7644 (t80) cc_final: 0.7404 (t80) REVERT: B 318 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8600 (ttpt) REVERT: B 487 ARG cc_start: 0.4776 (mtt90) cc_final: 0.3187 (mtp180) REVERT: B 541 LEU cc_start: 0.8500 (mm) cc_final: 0.8219 (tt) REVERT: C 268 LEU cc_start: 0.9237 (tp) cc_final: 0.8978 (tp) REVERT: C 318 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8603 (ttpt) REVERT: C 545 LYS cc_start: 0.6945 (mmtt) cc_final: 0.6345 (mmpt) REVERT: C 580 GLN cc_start: 0.8494 (tt0) cc_final: 0.8058 (tt0) REVERT: C 599 LEU cc_start: 0.8594 (mm) cc_final: 0.7895 (tt) REVERT: A 193 PHE cc_start: 0.7575 (t80) cc_final: 0.7328 (t80) REVERT: A 268 LEU cc_start: 0.9329 (tp) cc_final: 0.8986 (tp) REVERT: A 318 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8624 (ttpt) REVERT: A 371 ARG cc_start: 0.8441 (mtp-110) cc_final: 0.8179 (ttp-110) REVERT: A 580 GLN cc_start: 0.8573 (tt0) cc_final: 0.8155 (tt0) REVERT: A 690 ARG cc_start: 0.8033 (ptp90) cc_final: 0.7706 (ptm160) REVERT: D 318 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8632 (ttpt) REVERT: D 521 TRP cc_start: 0.8643 (m-10) cc_final: 0.7569 (m100) REVERT: D 591 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8420 (mm) outliers start: 64 outliers final: 63 residues processed: 401 average time/residue: 0.2669 time to fit residues: 166.1984 Evaluate side-chains 427 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 363 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 694 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108586 restraints weight = 35496.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111795 restraints weight = 21026.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113940 restraints weight = 15235.539| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18839 Z= 0.189 Angle : 0.617 14.634 25660 Z= 0.305 Chirality : 0.039 0.323 3064 Planarity : 0.003 0.043 3145 Dihedral : 10.730 89.778 2706 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.92 % Allowed : 28.65 % Favored : 67.44 % 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: 0.45 (0.18), residues: 2392 helix: 1.62 (0.13), residues: 1504 sheet: -3.02 (0.45), residues: 64 loop : -2.00 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 380 HIS 0.023 0.002 HIS C 160 PHE 0.015 0.001 PHE D 157 TYR 0.045 0.001 TYR A 594 ARG 0.006 0.000 ARG D 690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4176.98 seconds wall clock time: 76 minutes 50.43 seconds (4610.43 seconds total)