Starting phenix.real_space_refine on Sun Mar 17 06:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvf_30218/03_2024/7bvf_30218_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvf_30218/03_2024/7bvf_30218.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvf_30218/03_2024/7bvf_30218_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvf_30218/03_2024/7bvf_30218_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvf_30218/03_2024/7bvf_30218_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvf_30218/03_2024/7bvf_30218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvf_30218/03_2024/7bvf_30218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvf_30218/03_2024/7bvf_30218_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bvf_30218/03_2024/7bvf_30218_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.069 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 5 5.49 5 S 55 5.16 5 C 10982 2.51 5 N 2875 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 468": "NH1" <-> "NH2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 562": "NH1" <-> "NH2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "B ARG 697": "NH1" <-> "NH2" Residue "B TYR 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 751": "OD1" <-> "OD2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "B GLU 800": "OE1" <-> "OE2" Residue "B ASP 870": "OD1" <-> "OD2" Residue "B GLU 901": "OE1" <-> "OE2" Residue "B ASP 920": "OD1" <-> "OD2" Residue "B ASP 942": "OD1" <-> "OD2" Residue "B ASP 959": "OD1" <-> "OD2" Residue "B ASP 987": "OD1" <-> "OD2" Residue "B PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1008": "OE1" <-> "OE2" Residue "B ASP 1024": "OD1" <-> "OD2" Residue "B ASP 1026": "OD1" <-> "OD2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B ARG 1045": "NH1" <-> "NH2" Residue "B ASP 1072": "OD1" <-> "OD2" Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A ARG 501": "NH1" <-> "NH2" Residue "A TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A ASP 1067": "OD1" <-> "OD2" Residue "P GLU 6": "OE1" <-> "OE2" Residue "P ASP 40": "OD1" <-> "OD2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P ASP 61": "OD1" <-> "OD2" Residue "P GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16933 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 7993 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 969} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 8128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8128 Classifications: {'peptide': 1087} Link IDs: {'PCIS': 2, 'PTRANS': 78, 'TRANS': 1006} Chain: "P" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 607 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "B" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 127 Unusual residues: {' CA': 1, '95E': 1, 'CDL': 1, 'DSL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'DSL:plan-3': 1, 'DSL:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Time building chain proxies: 9.41, per 1000 atoms: 0.56 Number of scatterers: 16933 At special positions: 0 Unit cell: (132.02, 119.72, 121.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 55 16.00 P 5 15.00 O 3015 8.00 N 2875 7.00 C 10982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.61 Conformation dependent library (CDL) restraints added in 3.0 seconds 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 18 sheets defined 36.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'B' and resid 25 through 39 removed outlier: 3.963A pdb=" N VAL B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 137 through 140 No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 216 through 239 removed outlier: 3.994A pdb=" N ALA B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 293 removed outlier: 3.646A pdb=" N TRP B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 308 Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.780A pdb=" N LEU B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 350 No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'B' and resid 353 through 368 removed outlier: 3.746A pdb=" N GLY B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.023A pdb=" N ALA B 409 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 412 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 414 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 415 " --> pdb=" O SER B 412 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET B 423 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 425 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 removed outlier: 4.041A pdb=" N VAL B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.585A pdb=" N ARG B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 No H-bonds generated for 'chain 'B' and resid 476 through 479' Processing helix chain 'B' and resid 481 through 484 No H-bonds generated for 'chain 'B' and resid 481 through 484' Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 518 through 529 removed outlier: 3.692A pdb=" N GLU B 521 " --> pdb=" O TRP B 518 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN B 522 " --> pdb=" O TYR B 519 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR B 527 " --> pdb=" O ARG B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 559 removed outlier: 4.143A pdb=" N PHE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 546 " --> pdb=" O GLY B 542 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 549 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 554 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 586 removed outlier: 3.682A pdb=" N MET B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET B 586 " --> pdb=" O MET B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 600 removed outlier: 3.965A pdb=" N LEU B 598 " --> pdb=" O HIS B 595 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE B 599 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 600 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 613 removed outlier: 3.576A pdb=" N ALA B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 612 " --> pdb=" O ALA B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 639 Processing helix chain 'B' and resid 663 through 665 No H-bonds generated for 'chain 'B' and resid 663 through 665' Processing helix chain 'B' and resid 668 through 687 Processing helix chain 'B' and resid 697 through 701 Processing helix chain 'B' and resid 706 through 727 removed outlier: 3.595A pdb=" N MET B 722 " --> pdb=" O PHE B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 743 removed outlier: 3.564A pdb=" N VAL B 740 " --> pdb=" O GLY B 736 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE B 743 " --> pdb=" O ASN B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 751 removed outlier: 3.693A pdb=" N ASP B 751 " --> pdb=" O GLY B 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 751' Processing helix chain 'B' and resid 813 through 815 No H-bonds generated for 'chain 'B' and resid 813 through 815' Processing helix chain 'B' and resid 974 through 977 No H-bonds generated for 'chain 'B' and resid 974 through 977' Processing helix chain 'B' and resid 1018 through 1023 Processing helix chain 'B' and resid 1025 through 1028 No H-bonds generated for 'chain 'B' and resid 1025 through 1028' Processing helix chain 'B' and resid 1031 through 1033 No H-bonds generated for 'chain 'B' and resid 1031 through 1033' Processing helix chain 'B' and resid 1040 through 1043 No H-bonds generated for 'chain 'B' and resid 1040 through 1043' Processing helix chain 'A' and resid 11 through 27 removed outlier: 3.905A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 76 through 79 No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 206 through 229 removed outlier: 4.481A pdb=" N VAL A 211 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.943A pdb=" N ASP A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.937A pdb=" N GLN A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 324 No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 327 through 346 removed outlier: 3.988A pdb=" N GLY A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 339 " --> pdb=" O CYS A 335 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ARG A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 removed outlier: 3.875A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 402 removed outlier: 4.111A pdb=" N ALA A 386 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 389 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 402 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.697A pdb=" N ILE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 445 removed outlier: 4.130A pdb=" N LEU A 426 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) Proline residue: A 431 - end of helix removed outlier: 3.992A pdb=" N GLY A 435 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 436 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ALA A 438 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 441 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 444 " --> pdb=" O GLN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 removed outlier: 3.655A pdb=" N VAL A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 467 through 470 No H-bonds generated for 'chain 'A' and resid 467 through 470' Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 518 through 536 removed outlier: 3.659A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 531 " --> pdb=" O CYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 565 removed outlier: 4.812A pdb=" N THR A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 594 removed outlier: 4.149A pdb=" N ALA A 576 " --> pdb=" O GLN A 573 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 577 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 578 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLY A 579 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 581 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 582 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 592 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 593 " --> pdb=" O PHE A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 619 removed outlier: 3.578A pdb=" N VAL A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 669 removed outlier: 3.677A pdb=" N LEU A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP A 669 " --> pdb=" O HIS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 690 through 711 removed outlier: 3.502A pdb=" N SER A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 726 removed outlier: 3.989A pdb=" N ASN A 722 " --> pdb=" O THR A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 836 No H-bonds generated for 'chain 'A' and resid 834 through 836' Processing helix chain 'A' and resid 967 through 970 No H-bonds generated for 'chain 'A' and resid 967 through 970' Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 1011 through 1016 removed outlier: 3.560A pdb=" N ALA A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1021 No H-bonds generated for 'chain 'A' and resid 1018 through 1021' Processing helix chain 'A' and resid 1029 through 1031 No H-bonds generated for 'chain 'A' and resid 1029 through 1031' Processing helix chain 'P' and resid 12 through 20 removed outlier: 3.636A pdb=" N GLU P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 26 No H-bonds generated for 'chain 'P' and resid 24 through 26' Processing helix chain 'P' and resid 41 through 54 removed outlier: 3.826A pdb=" N GLU P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP P 53 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 80 Processing sheet with id= A, first strand: chain 'B' and resid 212 through 214 Processing sheet with id= B, first strand: chain 'B' and resid 78 through 81 removed outlier: 3.909A pdb=" N ASP B 78 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 205 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 115 through 117 removed outlier: 3.624A pdb=" N PHE B 115 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 753 through 756 removed outlier: 4.696A pdb=" N ALA B1050 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 874 through 877 Processing sheet with id= F, first strand: chain 'B' and resid 879 through 881 Processing sheet with id= G, first strand: chain 'B' and resid 984 through 986 removed outlier: 6.755A pdb=" N PHE B1012 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B1015 " --> pdb=" O SER B1063 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 901 through 904 removed outlier: 3.930A pdb=" N ALA B 945 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= J, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.572A pdb=" N ALA A 187 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 71 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 69 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 148 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 57 through 59 Processing sheet with id= L, first strand: chain 'A' and resid 107 through 109 Processing sheet with id= M, first strand: chain 'A' and resid 739 through 742 removed outlier: 4.253A pdb=" N ALA A1043 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 850 through 853 Processing sheet with id= O, first strand: chain 'A' and resid 868 through 873 Processing sheet with id= P, first strand: chain 'A' and resid 896 through 899 removed outlier: 3.634A pdb=" N TRP A 896 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 908 " --> pdb=" O TRP A 896 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 977 through 979 removed outlier: 7.171A pdb=" N TYR A1005 " --> pdb=" O LEU A 978 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 1037 through 1039 479 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.53 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 2645 1.25 - 1.39: 4119 1.39 - 1.53: 9487 1.53 - 1.67: 1024 1.67 - 1.81: 96 Bond restraints: 17371 Sorted by residual: bond pdb=" C ILE A 43 " pdb=" O ILE A 43 " ideal model delta sigma weight residual 1.237 1.119 0.118 1.08e-02 8.57e+03 1.20e+02 bond pdb=" CA7 CDL A1101 " pdb=" OA8 CDL A1101 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" OB3 CDL A1101 " pdb=" PB2 CDL A1101 " ideal model delta sigma weight residual 1.529 1.424 0.105 1.00e-02 1.00e+04 1.10e+02 bond pdb=" CB7 CDL A1101 " pdb=" OB8 CDL A1101 " ideal model delta sigma weight residual 1.334 1.437 -0.103 1.10e-02 8.26e+03 8.71e+01 bond pdb=" CA5 CDL B1404 " pdb=" OA6 CDL B1404 " ideal model delta sigma weight residual 1.342 1.469 -0.127 1.50e-02 4.44e+03 7.14e+01 ... (remaining 17366 not shown) Histogram of bond angle deviations from ideal: 92.78 - 101.09: 45 101.09 - 109.40: 1989 109.40 - 117.71: 10933 117.71 - 126.03: 10360 126.03 - 134.34: 438 Bond angle restraints: 23765 Sorted by residual: angle pdb=" C36 DSL B1403 " pdb=" C37 DSL B1403 " pdb=" C38 DSL B1403 " ideal model delta sigma weight residual 74.48 121.90 -47.42 3.00e+00 1.11e-01 2.50e+02 angle pdb=" C46 DSL B1403 " pdb=" C47 DSL B1403 " pdb=" C48 DSL B1403 " ideal model delta sigma weight residual 74.51 120.52 -46.01 3.00e+00 1.11e-01 2.35e+02 angle pdb=" C26 DSL B1403 " pdb=" C27 DSL B1403 " pdb=" C28 DSL B1403 " ideal model delta sigma weight residual 74.51 119.62 -45.11 3.00e+00 1.11e-01 2.26e+02 angle pdb=" C16 DSL B1403 " pdb=" C17 DSL B1403 " pdb=" C18 DSL B1403 " ideal model delta sigma weight residual 74.48 117.03 -42.55 3.00e+00 1.11e-01 2.01e+02 angle pdb=" C41 DSL B1403 " pdb=" C42 DSL B1403 " pdb=" C43 DSL B1403 " ideal model delta sigma weight residual 74.50 116.83 -42.33 3.00e+00 1.11e-01 1.99e+02 ... (remaining 23760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 10007 32.69 - 65.37: 229 65.37 - 98.06: 14 98.06 - 130.75: 1 130.75 - 163.43: 1 Dihedral angle restraints: 10252 sinusoidal: 3946 harmonic: 6306 Sorted by residual: dihedral pdb=" CA TRP B 58 " pdb=" C TRP B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta harmonic sigma weight residual -180.00 -53.49 -126.51 0 5.00e+00 4.00e-02 6.40e+02 dihedral pdb=" C PRO B 59 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " pdb=" CB PRO B 59 " ideal model delta harmonic sigma weight residual -120.70 -141.90 21.20 0 2.50e+00 1.60e-01 7.19e+01 dihedral pdb=" C THR B 732 " pdb=" N THR B 732 " pdb=" CA THR B 732 " pdb=" CB THR B 732 " ideal model delta harmonic sigma weight residual -122.00 -141.68 19.68 0 2.50e+00 1.60e-01 6.20e+01 ... (remaining 10249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 2743 0.234 - 0.468: 6 0.468 - 0.702: 1 0.702 - 0.937: 0 0.937 - 1.171: 1 Chirality restraints: 2751 Sorted by residual: chirality pdb=" CA PRO B 59 " pdb=" N PRO B 59 " pdb=" C PRO B 59 " pdb=" CB PRO B 59 " both_signs ideal model delta sigma weight residual False 2.72 1.55 1.17 2.00e-01 2.50e+01 3.43e+01 chirality pdb=" CA THR B 732 " pdb=" N THR B 732 " pdb=" C THR B 732 " pdb=" CB THR B 732 " both_signs ideal model delta sigma weight residual False 2.53 1.87 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA TYR B 730 " pdb=" N TYR B 730 " pdb=" C TYR B 730 " pdb=" CB TYR B 730 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 2748 not shown) Planarity restraints: 3018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 56 " -0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C LEU B 56 " 0.082 2.00e-02 2.50e+03 pdb=" O LEU B 56 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP B 57 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 730 " 0.048 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR B 730 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR B 730 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR B 730 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 730 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 730 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 730 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 730 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 731 " -0.016 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C PRO B 731 " 0.059 2.00e-02 2.50e+03 pdb=" O PRO B 731 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 732 " -0.020 2.00e-02 2.50e+03 ... (remaining 3015 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 3 2.11 - 2.81: 4879 2.81 - 3.50: 20852 3.50 - 4.20: 37839 4.20 - 4.90: 70038 Nonbonded interactions: 133611 Sorted by model distance: nonbonded pdb=" C LEU B 56 " pdb=" OD1 ASP B 57 " model vdw 1.409 3.270 nonbonded pdb=" O LEU B 56 " pdb=" OD1 ASP B 57 " model vdw 1.728 3.040 nonbonded pdb=" N ASP B 57 " pdb=" OD1 ASP B 57 " model vdw 2.075 2.520 nonbonded pdb=" OH TYR B 302 " pdb=" OD1 ASN B 318 " model vdw 2.184 2.440 nonbonded pdb=" NH1 ARG A 119 " pdb=" O LYS A 167 " model vdw 2.213 2.520 ... (remaining 133606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.350 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 46.310 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 17371 Z= 0.461 Angle : 1.251 47.424 23765 Z= 0.598 Chirality : 0.057 1.171 2751 Planarity : 0.006 0.074 3018 Dihedral : 14.108 163.434 6220 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.74 % Favored : 87.08 % Rotamer: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.93 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.15), residues: 2213 helix: -2.01 (0.16), residues: 802 sheet: -3.52 (0.28), residues: 249 loop : -3.91 (0.14), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 58 HIS 0.003 0.001 HIS B1047 PHE 0.019 0.001 PHE A 954 TYR 0.048 0.002 TYR B 730 ARG 0.005 0.000 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 1.807 Fit side-chains revert: symmetry clash REVERT: B 57 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.6738 (p0) REVERT: B 124 ASP cc_start: 0.7616 (p0) cc_final: 0.7353 (p0) REVERT: A 120 ASP cc_start: 0.6813 (p0) cc_final: 0.6579 (p0) REVERT: P 14 GLU cc_start: 0.7136 (tp30) cc_final: 0.6934 (tp30) outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 1.4213 time to fit residues: 320.3600 Evaluate side-chains 162 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 59 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 173 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 200 optimal weight: 0.2980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN B 296 ASN ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 ASN B 791 ASN B1077 GLN A 111 GLN A 377 ASN A 441 GLN A 598 HIS A 919 GLN A1004 GLN P 5 GLN P 78 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17371 Z= 0.172 Angle : 0.871 22.408 23765 Z= 0.369 Chirality : 0.043 0.173 2751 Planarity : 0.006 0.161 3018 Dihedral : 10.048 177.818 2581 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.30 % Favored : 89.56 % Rotamer: Outliers : 1.50 % Allowed : 10.78 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -3.64 (0.16), residues: 2213 helix: -1.13 (0.18), residues: 794 sheet: -2.80 (0.30), residues: 247 loop : -3.37 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 58 HIS 0.002 0.000 HIS A 140 PHE 0.008 0.001 PHE B 713 TYR 0.010 0.001 TYR B 526 ARG 0.006 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.994 Fit side-chains revert: symmetry clash REVERT: B 124 ASP cc_start: 0.7436 (p0) cc_final: 0.7104 (p0) REVERT: B 462 MET cc_start: 0.8439 (tpt) cc_final: 0.8042 (tpt) REVERT: B 464 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7504 (ttm-80) REVERT: B 482 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: A 681 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6882 (ttt180) outliers start: 26 outliers final: 10 residues processed: 207 average time/residue: 1.1904 time to fit residues: 277.4553 Evaluate side-chains 176 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain P residue 55 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN A 47 GLN A 110 ASN A 265 HIS A 441 GLN A 890 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17371 Z= 0.365 Angle : 0.939 22.109 23765 Z= 0.410 Chirality : 0.048 0.243 2751 Planarity : 0.007 0.158 3018 Dihedral : 9.587 169.593 2576 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.56 % Favored : 87.30 % Rotamer: Outliers : 3.17 % Allowed : 12.68 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -3.47 (0.16), residues: 2213 helix: -1.15 (0.18), residues: 803 sheet: -2.72 (0.31), residues: 246 loop : -3.16 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1054 HIS 0.003 0.001 HIS B1002 PHE 0.020 0.001 PHE A 954 TYR 0.015 0.002 TYR B 526 ARG 0.009 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 176 time to evaluate : 1.678 Fit side-chains REVERT: B 464 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7503 (ttm-80) REVERT: B 471 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7562 (mtp180) REVERT: B 889 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8458 (pt) REVERT: A 120 ASP cc_start: 0.6851 (p0) cc_final: 0.6589 (p0) REVERT: A 598 HIS cc_start: 0.6966 (p90) cc_final: 0.6628 (m-70) REVERT: A 681 ARG cc_start: 0.7231 (ttp80) cc_final: 0.6904 (ttt180) REVERT: P 62 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7100 (mp0) outliers start: 55 outliers final: 26 residues processed: 208 average time/residue: 1.1443 time to fit residues: 269.2016 Evaluate side-chains 196 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 840 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN A 441 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 17371 Z= 0.393 Angle : 0.949 21.987 23765 Z= 0.417 Chirality : 0.048 0.248 2751 Planarity : 0.007 0.162 3018 Dihedral : 9.388 162.499 2576 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.61 % Favored : 87.26 % Rotamer: Outliers : 3.52 % Allowed : 14.29 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -3.36 (0.17), residues: 2213 helix: -1.17 (0.18), residues: 807 sheet: -2.53 (0.32), residues: 241 loop : -3.03 (0.16), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1054 HIS 0.003 0.001 HIS B1047 PHE 0.020 0.002 PHE A 954 TYR 0.015 0.002 TYR B 526 ARG 0.007 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 172 time to evaluate : 2.044 Fit side-chains REVERT: B 471 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7545 (mtp180) REVERT: B 889 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8550 (pt) REVERT: A 120 ASP cc_start: 0.6960 (p0) cc_final: 0.6683 (p0) REVERT: A 598 HIS cc_start: 0.6957 (p90) cc_final: 0.6616 (m-70) REVERT: A 681 ARG cc_start: 0.7215 (ttp80) cc_final: 0.6950 (ttt180) REVERT: P 62 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7090 (mp0) outliers start: 61 outliers final: 34 residues processed: 211 average time/residue: 1.0959 time to fit residues: 262.0742 Evaluate side-chains 200 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 840 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 78 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 109 optimal weight: 0.3980 chunk 191 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 441 GLN A 990 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17371 Z= 0.181 Angle : 0.864 21.554 23765 Z= 0.364 Chirality : 0.043 0.215 2751 Planarity : 0.006 0.164 3018 Dihedral : 8.492 155.711 2576 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.44 % Favored : 89.47 % Rotamer: Outliers : 2.77 % Allowed : 16.37 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.17), residues: 2213 helix: -0.78 (0.19), residues: 793 sheet: -2.09 (0.32), residues: 242 loop : -2.82 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1054 HIS 0.002 0.000 HIS A 140 PHE 0.009 0.001 PHE B 688 TYR 0.009 0.001 TYR A 626 ARG 0.005 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 1.798 Fit side-chains REVERT: A 11 ARG cc_start: 0.6593 (mpt180) cc_final: 0.6345 (mpt180) REVERT: A 598 HIS cc_start: 0.6882 (p90) cc_final: 0.6555 (m-70) REVERT: A 681 ARG cc_start: 0.7232 (ttp80) cc_final: 0.6940 (ttt180) outliers start: 48 outliers final: 21 residues processed: 213 average time/residue: 1.0997 time to fit residues: 267.0285 Evaluate side-chains 193 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 969 ARG Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 3.9990 chunk 192 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 HIS ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS A 441 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 17371 Z= 0.193 Angle : 0.864 21.637 23765 Z= 0.363 Chirality : 0.043 0.220 2751 Planarity : 0.006 0.164 3018 Dihedral : 8.122 153.002 2576 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.62 % Favored : 89.29 % Rotamer: Outliers : 2.42 % Allowed : 17.35 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.17), residues: 2213 helix: -0.59 (0.19), residues: 794 sheet: -1.94 (0.33), residues: 237 loop : -2.69 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1054 HIS 0.002 0.001 HIS A 140 PHE 0.011 0.001 PHE A 954 TYR 0.010 0.001 TYR A 626 ARG 0.004 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 1.947 Fit side-chains REVERT: B 471 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7523 (mtp180) REVERT: B 889 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8514 (pt) REVERT: A 11 ARG cc_start: 0.6658 (mpt180) cc_final: 0.6372 (mpt180) REVERT: A 598 HIS cc_start: 0.6899 (p90) cc_final: 0.6563 (m-70) REVERT: A 681 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6922 (ttt180) REVERT: A 781 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7400 (mt) REVERT: P 62 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6986 (mp0) outliers start: 42 outliers final: 20 residues processed: 206 average time/residue: 1.1306 time to fit residues: 263.8683 Evaluate side-chains 197 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 969 ARG Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 17371 Z= 0.179 Angle : 0.854 21.561 23765 Z= 0.356 Chirality : 0.043 0.225 2751 Planarity : 0.006 0.162 3018 Dihedral : 7.861 151.724 2576 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.12 % Favored : 89.83 % Rotamer: Outliers : 2.02 % Allowed : 18.21 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.17), residues: 2213 helix: -0.43 (0.19), residues: 794 sheet: -1.76 (0.33), residues: 241 loop : -2.58 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1054 HIS 0.002 0.000 HIS B 470 PHE 0.009 0.001 PHE B 688 TYR 0.008 0.001 TYR A 626 ARG 0.002 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 1.903 Fit side-chains REVERT: B 471 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7521 (mtp180) REVERT: B 722 MET cc_start: 0.8476 (mmt) cc_final: 0.8219 (mmt) REVERT: A 11 ARG cc_start: 0.6697 (mpt180) cc_final: 0.6396 (mpt180) REVERT: A 598 HIS cc_start: 0.6897 (p90) cc_final: 0.6550 (m-70) REVERT: P 62 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6975 (mp0) outliers start: 35 outliers final: 24 residues processed: 208 average time/residue: 1.0835 time to fit residues: 255.9375 Evaluate side-chains 203 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 969 ARG Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 127 optimal weight: 0.0170 chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 135 optimal weight: 0.3980 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 0.0470 chunk 19 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 17371 Z= 0.167 Angle : 0.853 21.520 23765 Z= 0.356 Chirality : 0.043 0.223 2751 Planarity : 0.006 0.162 3018 Dihedral : 7.641 150.981 2576 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.72 % Favored : 90.24 % Rotamer: Outliers : 1.90 % Allowed : 18.85 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 2213 helix: -0.24 (0.19), residues: 795 sheet: -1.63 (0.33), residues: 241 loop : -2.45 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 663 HIS 0.002 0.000 HIS B 470 PHE 0.009 0.001 PHE B 688 TYR 0.008 0.001 TYR A 626 ARG 0.003 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.829 Fit side-chains REVERT: B 722 MET cc_start: 0.8475 (mmt) cc_final: 0.8183 (mmt) REVERT: B 867 LYS cc_start: 0.8259 (tppt) cc_final: 0.8055 (mmtm) REVERT: A 598 HIS cc_start: 0.6899 (p90) cc_final: 0.6509 (m-70) REVERT: P 62 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6973 (mp0) outliers start: 33 outliers final: 23 residues processed: 202 average time/residue: 1.1587 time to fit residues: 265.6904 Evaluate side-chains 201 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 969 ARG Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 ASN A 140 HIS A 441 GLN A 822 ASN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17371 Z= 0.203 Angle : 0.869 21.607 23765 Z= 0.365 Chirality : 0.044 0.228 2751 Planarity : 0.006 0.161 3018 Dihedral : 7.716 151.830 2576 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.53 % Favored : 89.43 % Rotamer: Outliers : 2.19 % Allowed : 18.90 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.18), residues: 2213 helix: -0.23 (0.19), residues: 794 sheet: -1.57 (0.33), residues: 241 loop : -2.43 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 663 HIS 0.002 0.000 HIS A 140 PHE 0.016 0.001 PHE A 499 TYR 0.009 0.001 TYR A 626 ARG 0.006 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 1.883 Fit side-chains REVERT: B 722 MET cc_start: 0.8498 (mmt) cc_final: 0.8191 (mmt) REVERT: B 867 LYS cc_start: 0.8248 (tppt) cc_final: 0.8037 (mmtm) REVERT: A 11 ARG cc_start: 0.6714 (mpt180) cc_final: 0.6397 (mpt180) REVERT: A 598 HIS cc_start: 0.6938 (p90) cc_final: 0.6524 (m-70) REVERT: P 14 GLU cc_start: 0.7009 (tp30) cc_final: 0.6749 (tp30) REVERT: P 62 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7047 (mp0) outliers start: 38 outliers final: 23 residues processed: 200 average time/residue: 1.1391 time to fit residues: 257.4976 Evaluate side-chains 192 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 139 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17371 Z= 0.218 Angle : 0.878 21.653 23765 Z= 0.371 Chirality : 0.044 0.233 2751 Planarity : 0.006 0.160 3018 Dihedral : 7.779 152.191 2576 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.62 % Favored : 89.34 % Rotamer: Outliers : 1.50 % Allowed : 19.83 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.18), residues: 2213 helix: -0.20 (0.19), residues: 795 sheet: -1.59 (0.34), residues: 233 loop : -2.39 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 663 HIS 0.003 0.001 HIS A 140 PHE 0.012 0.001 PHE A 954 TYR 0.010 0.001 TYR B 526 ARG 0.008 0.000 ARG B 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.863 Fit side-chains REVERT: A 11 ARG cc_start: 0.6719 (mpt180) cc_final: 0.6376 (mpt180) REVERT: A 598 HIS cc_start: 0.6936 (p90) cc_final: 0.6515 (m-70) REVERT: A 781 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7282 (mt) REVERT: P 62 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7053 (mp0) outliers start: 26 outliers final: 21 residues processed: 185 average time/residue: 1.1657 time to fit residues: 245.3931 Evaluate side-chains 190 residues out of total 1737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS A 441 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108366 restraints weight = 21330.398| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.58 r_work: 0.3102 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17371 Z= 0.206 Angle : 0.873 21.638 23765 Z= 0.367 Chirality : 0.044 0.234 2751 Planarity : 0.006 0.160 3018 Dihedral : 7.745 151.786 2576 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.48 % Favored : 89.47 % Rotamer: Outliers : 1.61 % Allowed : 19.65 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.18), residues: 2213 helix: -0.08 (0.19), residues: 789 sheet: -1.55 (0.33), residues: 235 loop : -2.37 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1054 HIS 0.003 0.001 HIS A 140 PHE 0.025 0.001 PHE A 499 TYR 0.010 0.001 TYR B 526 ARG 0.008 0.000 ARG B 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5330.42 seconds wall clock time: 95 minutes 5.66 seconds (5705.66 seconds total)