Starting phenix.real_space_refine on Mon Feb 19 12:15:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2024/7mca_23755_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2024/7mca_23755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2024/7mca_23755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2024/7mca_23755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2024/7mca_23755_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2024/7mca_23755_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 112 5.49 5 Mg 4 5.21 5 S 104 5.16 5 C 15509 2.51 5 N 4145 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 683": "NH1" <-> "NH2" Residue "A GLU 690": "OE1" <-> "OE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 834": "OE1" <-> "OE2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "A ARG 912": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B ARG 433": "NH1" <-> "NH2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 193": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ARG 365": "NH1" <-> "NH2" Residue "E ARG 366": "NH1" <-> "NH2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E GLU 464": "OE1" <-> "OE2" Residue "F GLU 284": "OE1" <-> "OE2" Residue "F ARG 287": "NH1" <-> "NH2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "F ARG 380": "NH1" <-> "NH2" Residue "F ARG 385": "NH1" <-> "NH2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 274": "NH1" <-> "NH2" Residue "I PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 404": "NH1" <-> "NH2" Residue "I GLU 435": "OE1" <-> "OE2" Residue "I ARG 455": "NH1" <-> "NH2" Residue "I GLU 497": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24692 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 483} Chain breaks: 3 Chain: "B" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2096 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain breaks: 1 Chain: "C" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4830 Classifications: {'peptide': 584} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3572 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 3 Chain: "E" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3702 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1369 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "G" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1018 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "H" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1032 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2999 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 12, 'TRANS': 363} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.16, per 1000 atoms: 0.53 Number of scatterers: 24692 At special positions: 0 Unit cell: (117.576, 138.276, 182.988, 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) S 104 16.00 P 112 15.00 Mg 4 11.99 O 4818 8.00 N 4145 7.00 C 15509 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.06 Conformation dependent library (CDL) restraints added in 3.8 seconds 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5354 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 125 helices and 11 sheets defined 41.4% alpha, 4.7% beta 21 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 9.98 Creating SS restraints... Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 456 through 467 removed outlier: 4.400A pdb=" N ALA A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 502 Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 539 through 551 Processing helix chain 'A' and resid 577 through 584 removed outlier: 3.668A pdb=" N PHE A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 686 through 698 removed outlier: 4.186A pdb=" N LYS A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 725 removed outlier: 3.653A pdb=" N ALA A 714 " --> pdb=" O CYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 783 removed outlier: 5.476A pdb=" N LYS A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 794 No H-bonds generated for 'chain 'A' and resid 791 through 794' Processing helix chain 'A' and resid 799 through 815 removed outlier: 3.600A pdb=" N MET A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 814 " --> pdb=" O ASN A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 840 through 851 removed outlier: 4.229A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 874 removed outlier: 3.746A pdb=" N LEU A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 904 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 271 through 283 removed outlier: 3.649A pdb=" N ASN B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 removed outlier: 3.955A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 372 through 382 removed outlier: 3.559A pdb=" N ASP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 removed outlier: 3.784A pdb=" N LYS B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.532A pdb=" N SER B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'C' and resid 51 through 90 removed outlier: 3.954A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 155 Processing helix chain 'C' and resid 186 through 189 No H-bonds generated for 'chain 'C' and resid 186 through 189' Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.628A pdb=" N ASN C 218 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.547A pdb=" N LEU C 285 " --> pdb=" O PHE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 318 through 329 removed outlier: 4.006A pdb=" N TYR C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 348 through 356 removed outlier: 3.760A pdb=" N ARG C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'C' and resid 374 through 381 removed outlier: 3.900A pdb=" N SER C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 396 removed outlier: 3.548A pdb=" N PHE C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 396 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 414 Processing helix chain 'C' and resid 424 through 433 Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 474 through 477 No H-bonds generated for 'chain 'C' and resid 474 through 477' Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 513 through 516 No H-bonds generated for 'chain 'C' and resid 513 through 516' Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 537 through 547 removed outlier: 3.637A pdb=" N PHE C 544 " --> pdb=" O PHE C 540 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 565 through 571 removed outlier: 3.907A pdb=" N LEU C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 591 removed outlier: 4.221A pdb=" N ILE C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 141 through 157 removed outlier: 3.750A pdb=" N GLN D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 229 through 239 removed outlier: 4.190A pdb=" N VAL D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 300 through 314 removed outlier: 4.110A pdb=" N SER D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN D 306 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR D 308 " --> pdb=" O TRP D 305 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS D 311 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER D 314 " --> pdb=" O LYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.501A pdb=" N GLU D 329 " --> pdb=" O ARG D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 347 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 351 through 360 Processing helix chain 'D' and resid 366 through 372 removed outlier: 4.129A pdb=" N LEU D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 408 through 424 removed outlier: 3.665A pdb=" N GLU D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 510 through 514 Processing helix chain 'D' and resid 524 through 527 Processing helix chain 'E' and resid 12 through 19 removed outlier: 3.717A pdb=" N ASN E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 70 through 86 removed outlier: 3.906A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 105 through 118 removed outlier: 4.119A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 removed outlier: 3.933A pdb=" N ILE E 150 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS E 151 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU E 152 " --> pdb=" O TYR E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 194 through 205 removed outlier: 4.069A pdb=" N THR E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 216 No H-bonds generated for 'chain 'E' and resid 213 through 216' Processing helix chain 'E' and resid 218 through 221 No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 229 through 246 removed outlier: 4.496A pdb=" N VAL E 235 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 removed outlier: 3.545A pdb=" N ASP E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 4.488A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 383 through 392 Processing helix chain 'E' and resid 418 through 429 Processing helix chain 'E' and resid 456 through 465 removed outlier: 4.128A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 291 Processing helix chain 'F' and resid 296 through 305 removed outlier: 4.097A pdb=" N LYS F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP F 304 " --> pdb=" O TYR F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 326 removed outlier: 4.134A pdb=" N VAL F 320 " --> pdb=" O PRO F 316 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS F 321 " --> pdb=" O TRP F 317 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 325 " --> pdb=" O CYS F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 341 through 353 removed outlier: 4.338A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 370 removed outlier: 4.019A pdb=" N GLU F 364 " --> pdb=" O ASP F 361 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL F 366 " --> pdb=" O ILE F 363 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 369 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS F 370 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 383 Processing helix chain 'F' and resid 394 through 401 removed outlier: 4.510A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 423 removed outlier: 4.270A pdb=" N ASN F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 90 Processing helix chain 'I' and resid 114 through 123 removed outlier: 3.578A pdb=" N MET I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 186 No H-bonds generated for 'chain 'I' and resid 184 through 186' Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 239 through 244 Processing helix chain 'I' and resid 293 through 302 Processing helix chain 'I' and resid 314 through 322 Processing helix chain 'I' and resid 331 through 348 removed outlier: 3.600A pdb=" N ASP I 336 " --> pdb=" O ARG I 332 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL I 337 " --> pdb=" O LYS I 333 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU I 338 " --> pdb=" O LEU I 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG I 339 " --> pdb=" O PHE I 335 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY I 340 " --> pdb=" O ASP I 336 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU I 347 " --> pdb=" O GLU I 343 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU I 348 " --> pdb=" O ILE I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 390 through 398 removed outlier: 3.811A pdb=" N SER I 395 " --> pdb=" O ALA I 391 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 409 removed outlier: 3.733A pdb=" N ILE I 407 " --> pdb=" O THR I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 422 Processing helix chain 'I' and resid 433 through 438 Processing helix chain 'I' and resid 455 through 468 removed outlier: 3.925A pdb=" N THR I 463 " --> pdb=" O LEU I 459 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE I 464 " --> pdb=" O GLU I 460 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 465 " --> pdb=" O ILE I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 503 removed outlier: 3.501A pdb=" N MET I 502 " --> pdb=" O PHE I 498 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR I 503 " --> pdb=" O TYR I 499 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 474 through 476 removed outlier: 8.030A pdb=" N ILE A 475 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL A 595 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 509 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU A 564 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 511 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP A 566 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 513 " --> pdb=" O ASP A 566 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 648 through 651 Processing sheet with id= C, first strand: chain 'A' and resid 682 through 684 removed outlier: 7.236A pdb=" N GLN A 771 " --> pdb=" O ARG A 683 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 879 through 881 Processing sheet with id= E, first strand: chain 'B' and resid 475 through 477 removed outlier: 6.663A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 235 through 240 removed outlier: 6.299A pdb=" N ASN C 103 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE C 238 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 105 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE C 240 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU C 107 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.586A pdb=" N ASP C 198 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL C 127 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA C 200 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE C 129 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 202 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU C 131 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN C 204 " --> pdb=" O LEU C 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 534 through 536 Processing sheet with id= I, first strand: chain 'D' and resid 271 through 274 removed outlier: 4.747A pdb=" N ARG D 271 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 99 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 212 " --> pdb=" O CYS D 246 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE D 216 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 58 through 62 removed outlier: 4.808A pdb=" N HIS E 58 " --> pdb=" O CYS E 127 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 433 through 435 603 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 7.79 Time building geometry restraints manager: 10.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 9510 1.38 - 1.55: 15478 1.55 - 1.73: 218 1.73 - 1.90: 165 1.90 - 2.08: 4 Bond restraints: 25375 Sorted by residual: bond pdb=" C4 AGS D2001 " pdb=" C5 AGS D2001 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.85e+01 bond pdb=" C5 AGS D2001 " pdb=" C6 AGS D2001 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" PG AGS D2001 " pdb=" S1G AGS D2001 " ideal model delta sigma weight residual 1.949 2.076 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C8 AGS D2001 " pdb=" N7 AGS D2001 " ideal model delta sigma weight residual 1.311 1.357 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" C5 AGS D2001 " pdb=" N7 AGS D2001 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.94e+01 ... (remaining 25370 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.40: 791 105.40 - 113.05: 13761 113.05 - 120.69: 11885 120.69 - 128.34: 8043 128.34 - 135.98: 247 Bond angle restraints: 34727 Sorted by residual: angle pdb=" C5 AGS D2001 " pdb=" C4 AGS D2001 " pdb=" N3 AGS D2001 " ideal model delta sigma weight residual 126.80 118.79 8.01 7.41e-01 1.82e+00 1.17e+02 angle pdb=" C4 AGS D2001 " pdb=" C5 AGS D2001 " pdb=" N7 AGS D2001 " ideal model delta sigma weight residual 110.73 106.70 4.03 4.52e-01 4.89e+00 7.95e+01 angle pdb=" C5 AGS D2001 " pdb=" N7 AGS D2001 " pdb=" C8 AGS D2001 " ideal model delta sigma weight residual 103.67 107.42 -3.75 4.26e-01 5.51e+00 7.74e+01 angle pdb=" N3 AGS D2001 " pdb=" C4 AGS D2001 " pdb=" N9 AGS D2001 " ideal model delta sigma weight residual 127.16 134.97 -7.81 1.06e+00 8.92e-01 5.44e+01 angle pdb=" C4 AGS D2001 " pdb=" N9 AGS D2001 " pdb=" C8 AGS D2001 " ideal model delta sigma weight residual 105.70 108.58 -2.88 4.55e-01 4.83e+00 4.01e+01 ... (remaining 34722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.57: 14262 33.57 - 67.14: 894 67.14 - 100.72: 43 100.72 - 134.29: 1 134.29 - 167.86: 1 Dihedral angle restraints: 15201 sinusoidal: 7000 harmonic: 8201 Sorted by residual: dihedral pdb=" CA GLU I 235 " pdb=" C GLU I 235 " pdb=" N THR I 236 " pdb=" CA THR I 236 " ideal model delta harmonic sigma weight residual -180.00 -137.59 -42.41 0 5.00e+00 4.00e-02 7.19e+01 dihedral pdb=" CA PHE I 126 " pdb=" C PHE I 126 " pdb=" N GLN I 127 " pdb=" CA GLN I 127 " ideal model delta harmonic sigma weight residual 180.00 -143.87 -36.13 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CA LEU I 282 " pdb=" C LEU I 282 " pdb=" N PRO I 283 " pdb=" CA PRO I 283 " ideal model delta harmonic sigma weight residual -180.00 -146.71 -33.29 0 5.00e+00 4.00e-02 4.43e+01 ... (remaining 15198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3334 0.078 - 0.155: 566 0.155 - 0.233: 49 0.233 - 0.310: 8 0.310 - 0.388: 3 Chirality restraints: 3960 Sorted by residual: chirality pdb=" CB ILE D 508 " pdb=" CA ILE D 508 " pdb=" CG1 ILE D 508 " pdb=" CG2 ILE D 508 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CB ILE A 622 " pdb=" CA ILE A 622 " pdb=" CG1 ILE A 622 " pdb=" CG2 ILE A 622 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB ILE B 432 " pdb=" CA ILE B 432 " pdb=" CG1 ILE B 432 " pdb=" CG2 ILE B 432 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3957 not shown) Planarity restraints: 4013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 214 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C LYS I 214 " 0.067 2.00e-02 2.50e+03 pdb=" O LYS I 214 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS I 215 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 454 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO E 455 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 455 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 455 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER I 395 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C SER I 395 " -0.051 2.00e-02 2.50e+03 pdb=" O SER I 395 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS I 396 " 0.017 2.00e-02 2.50e+03 ... (remaining 4010 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 13 1.82 - 2.59: 273 2.59 - 3.36: 30151 3.36 - 4.13: 60132 4.13 - 4.90: 109056 Nonbonded interactions: 199625 Sorted by model distance: nonbonded pdb=" O4 DT G 7 " pdb=" N1 DA H 79 " model vdw 1.053 2.496 nonbonded pdb=" N3 DT G 5 " pdb=" N1 DA H 81 " model vdw 1.099 2.600 nonbonded pdb=" O4 DT G 5 " pdb=" N6 DA H 81 " model vdw 1.161 2.520 nonbonded pdb=" O4 DT G 6 " pdb=" N1 DA H 80 " model vdw 1.375 2.496 nonbonded pdb=" O2 DT G 5 " pdb=" C2 DA H 81 " model vdw 1.508 3.340 ... (remaining 199620 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 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: 1.360 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: 5.740 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 69.100 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 25375 Z= 0.454 Angle : 0.979 15.601 34727 Z= 0.564 Chirality : 0.058 0.388 3960 Planarity : 0.006 0.076 4013 Dihedral : 19.391 167.859 9847 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.24 % Favored : 91.69 % Rotamer: Outliers : 0.75 % Allowed : 10.87 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.08 % 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: -5.13 (0.12), residues: 2718 helix: -3.47 (0.09), residues: 1379 sheet: -2.53 (0.33), residues: 197 loop : -3.33 (0.15), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 305 HIS 0.011 0.002 HIS D 96 PHE 0.051 0.002 PHE I 126 TYR 0.031 0.003 TYR C 483 ARG 0.008 0.001 ARG D 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 495 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9136 (tp) cc_final: 0.8843 (tt) REVERT: B 262 THR cc_start: 0.8177 (m) cc_final: 0.7775 (t) REVERT: B 380 THR cc_start: 0.7608 (p) cc_final: 0.7290 (t) REVERT: C 37 LYS cc_start: 0.6776 (tptt) cc_final: 0.6492 (tptt) REVERT: C 100 ARG cc_start: 0.6778 (mmt180) cc_final: 0.6422 (mpt180) REVERT: C 186 SER cc_start: 0.7665 (p) cc_final: 0.7144 (t) REVERT: C 421 ASN cc_start: 0.7769 (t0) cc_final: 0.7510 (t0) REVERT: C 469 ASP cc_start: 0.7527 (t0) cc_final: 0.5899 (t0) REVERT: D 284 MET cc_start: 0.8296 (mtp) cc_final: 0.8044 (mtp) REVERT: D 454 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7937 (mttt) REVERT: E 297 ASP cc_start: 0.6726 (m-30) cc_final: 0.6083 (p0) REVERT: F 273 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8484 (pp) REVERT: I 87 GLN cc_start: 0.3942 (tm-30) cc_final: 0.3586 (mt0) REVERT: I 226 ASP cc_start: 0.5007 (m-30) cc_final: 0.4743 (m-30) REVERT: I 268 LYS cc_start: 0.3708 (tppt) cc_final: 0.3221 (tttt) REVERT: I 334 LEU cc_start: 0.8162 (tp) cc_final: 0.7708 (tp) REVERT: I 484 ARG cc_start: 0.5035 (mtt90) cc_final: 0.4755 (mtm110) outliers start: 19 outliers final: 5 residues processed: 512 average time/residue: 0.4317 time to fit residues: 330.0298 Evaluate side-chains 281 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 275 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 409 LYS Chi-restraints excluded: chain I residue 418 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 600 ASN A 771 GLN A 820 GLN B 256 ASN B 284 ASN B 291 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN B 425 HIS B 493 GLN C 67 HIS C 178 ASN C 241 ASN C 331 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN C 523 GLN C 536 ASN D 137 HIS D 153 GLN D 306 ASN D 339 ASN D 370 ASN D 371 GLN D 409 ASN D 458 ASN D 507 GLN E 32 ASN E 52 ASN E 82 GLN E 113 HIS E 139 GLN E 193 ASN E 223 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 ASN I 99 HIS I 193 ASN ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 313 GLN I 388 ASN I 439 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25375 Z= 0.210 Angle : 0.615 12.915 34727 Z= 0.329 Chirality : 0.042 0.159 3960 Planarity : 0.004 0.058 4013 Dihedral : 19.352 173.541 4211 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.36 % Allowed : 15.94 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.85 (0.14), residues: 2718 helix: -2.18 (0.12), residues: 1362 sheet: -2.25 (0.35), residues: 197 loop : -2.98 (0.16), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 378 HIS 0.005 0.001 HIS C 22 PHE 0.055 0.001 PHE I 126 TYR 0.034 0.001 TYR I 291 ARG 0.005 0.000 ARG F 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 324 time to evaluate : 2.643 Fit side-chains revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9137 (tp) cc_final: 0.8824 (tt) REVERT: A 566 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: B 380 THR cc_start: 0.7760 (p) cc_final: 0.7463 (t) REVERT: C 37 LYS cc_start: 0.6865 (tptt) cc_final: 0.6584 (tptt) REVERT: C 98 LYS cc_start: 0.6415 (tptp) cc_final: 0.6028 (mtmm) REVERT: C 100 ARG cc_start: 0.6851 (mmt180) cc_final: 0.6644 (ptp-170) REVERT: C 241 ASN cc_start: 0.7068 (OUTLIER) cc_final: 0.6705 (t0) REVERT: D 284 MET cc_start: 0.8267 (mtp) cc_final: 0.8003 (mtp) REVERT: D 454 LYS cc_start: 0.8423 (ttpt) cc_final: 0.7898 (mttt) REVERT: D 471 GLU cc_start: 0.7490 (mp0) cc_final: 0.6918 (mp0) REVERT: D 512 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7111 (mt-10) REVERT: D 522 MET cc_start: 0.7329 (pmm) cc_final: 0.7093 (pmm) REVERT: E 297 ASP cc_start: 0.6751 (m-30) cc_final: 0.6163 (p0) REVERT: F 273 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8430 (pp) REVERT: F 368 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8296 (tt) REVERT: I 268 LYS cc_start: 0.3541 (tppt) cc_final: 0.3142 (tptm) REVERT: I 334 LEU cc_start: 0.8151 (tp) cc_final: 0.7787 (tp) REVERT: I 477 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8035 (mtpt) REVERT: I 502 MET cc_start: 0.3731 (mpp) cc_final: 0.3315 (mpp) outliers start: 60 outliers final: 29 residues processed: 363 average time/residue: 0.3599 time to fit residues: 205.0435 Evaluate side-chains 299 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 266 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 476 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 213 optimal weight: 0.0670 chunk 174 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 255 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN B 478 HIS B 493 GLN C 126 ASN C 178 ASN C 214 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN C 430 ASN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN D 446 ASN E 82 GLN E 139 GLN E 182 HIS E 223 GLN E 248 HIS ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 HIS I 204 HIS I 213 HIS I 232 ASN I 313 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25375 Z= 0.379 Angle : 0.676 11.857 34727 Z= 0.354 Chirality : 0.046 0.253 3960 Planarity : 0.004 0.051 4013 Dihedral : 19.383 170.156 4204 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.82 % Allowed : 17.83 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.50 (0.14), residues: 2718 helix: -1.76 (0.13), residues: 1352 sheet: -2.31 (0.35), residues: 186 loop : -2.96 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 58 HIS 0.019 0.002 HIS I 99 PHE 0.039 0.002 PHE I 126 TYR 0.020 0.002 TYR D 524 ARG 0.006 0.001 ARG D 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 283 time to evaluate : 2.772 Fit side-chains REVERT: A 422 ILE cc_start: 0.9204 (tp) cc_final: 0.8914 (tt) REVERT: A 566 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: A 808 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9064 (tt) REVERT: B 341 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8359 (t) REVERT: B 380 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7580 (t) REVERT: C 98 LYS cc_start: 0.6633 (tptp) cc_final: 0.6337 (ttmt) REVERT: C 100 ARG cc_start: 0.7053 (mmt180) cc_final: 0.6829 (ptp-170) REVERT: C 241 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6646 (t0) REVERT: D 113 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6925 (t0) REVERT: D 176 SER cc_start: 0.8618 (p) cc_final: 0.8410 (p) REVERT: D 454 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7964 (mttt) REVERT: D 471 GLU cc_start: 0.7669 (mp0) cc_final: 0.7112 (mp0) REVERT: D 493 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7488 (tm-30) REVERT: D 512 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7183 (mt-10) REVERT: D 514 ARG cc_start: 0.7617 (tpt170) cc_final: 0.7135 (ttt90) REVERT: D 522 MET cc_start: 0.7247 (pmm) cc_final: 0.6921 (pmm) REVERT: E 36 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8636 (tm-30) REVERT: E 297 ASP cc_start: 0.7068 (m-30) cc_final: 0.6204 (p0) REVERT: F 273 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8472 (pp) REVERT: I 268 LYS cc_start: 0.3565 (tppt) cc_final: 0.3170 (tptm) REVERT: I 318 LYS cc_start: 0.6415 (mmtt) cc_final: 0.5967 (pptt) REVERT: I 334 LEU cc_start: 0.8186 (tp) cc_final: 0.7801 (tp) REVERT: I 418 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7405 (tt) REVERT: I 477 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8031 (mtpt) outliers start: 97 outliers final: 58 residues processed: 356 average time/residue: 0.3436 time to fit residues: 196.2480 Evaluate side-chains 324 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 258 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 254 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 258 optimal weight: 20.0000 chunk 273 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 178 ASN C 214 ASN C 241 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN E 82 GLN ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25375 Z= 0.184 Angle : 0.566 10.370 34727 Z= 0.299 Chirality : 0.041 0.166 3960 Planarity : 0.003 0.049 4013 Dihedral : 19.058 177.200 4204 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.28 % Favored : 92.68 % Rotamer: Outliers : 3.54 % Allowed : 19.13 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.98 (0.15), residues: 2718 helix: -1.27 (0.14), residues: 1356 sheet: -2.24 (0.35), residues: 199 loop : -2.75 (0.16), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 378 HIS 0.005 0.001 HIS C 22 PHE 0.035 0.001 PHE I 126 TYR 0.027 0.001 TYR I 291 ARG 0.003 0.000 ARG D 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 291 time to evaluate : 2.721 Fit side-chains REVERT: A 422 ILE cc_start: 0.9202 (tp) cc_final: 0.8924 (tt) REVERT: A 566 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: A 636 ILE cc_start: 0.7671 (mm) cc_final: 0.7446 (mm) REVERT: B 380 THR cc_start: 0.7842 (p) cc_final: 0.7573 (t) REVERT: B 447 ILE cc_start: 0.8628 (mt) cc_final: 0.8405 (mt) REVERT: C 100 ARG cc_start: 0.6992 (mmt180) cc_final: 0.6765 (ptp-170) REVERT: D 113 ASP cc_start: 0.7205 (t0) cc_final: 0.6912 (t0) REVERT: D 454 LYS cc_start: 0.8416 (ttpt) cc_final: 0.7942 (mtmt) REVERT: D 471 GLU cc_start: 0.7534 (mp0) cc_final: 0.7017 (mp0) REVERT: D 493 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7483 (tm-30) REVERT: D 512 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7028 (mt-10) REVERT: D 514 ARG cc_start: 0.7479 (tpt170) cc_final: 0.7101 (ttt90) REVERT: E 222 GLU cc_start: 0.7229 (mm-30) cc_final: 0.7007 (mm-30) REVERT: E 297 ASP cc_start: 0.6950 (m-30) cc_final: 0.6104 (p0) REVERT: F 296 ARG cc_start: 0.7699 (mtp85) cc_final: 0.7342 (ptp-110) REVERT: I 89 MET cc_start: 0.3417 (mmm) cc_final: 0.3181 (mmm) REVERT: I 268 LYS cc_start: 0.3410 (tppt) cc_final: 0.3109 (tttp) REVERT: I 318 LYS cc_start: 0.6349 (mmtt) cc_final: 0.6144 (pptt) REVERT: I 334 LEU cc_start: 0.8099 (tp) cc_final: 0.7749 (tp) REVERT: I 434 ASP cc_start: 0.4877 (OUTLIER) cc_final: 0.4645 (t0) REVERT: I 477 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7940 (mtpt) outliers start: 90 outliers final: 56 residues processed: 359 average time/residue: 0.3553 time to fit residues: 202.0464 Evaluate side-chains 324 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 266 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 482 ASN Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 227 optimal weight: 0.0020 chunk 155 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 178 ASN C 239 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN C 563 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 GLN ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25375 Z= 0.306 Angle : 0.623 11.937 34727 Z= 0.322 Chirality : 0.044 0.203 3960 Planarity : 0.004 0.048 4013 Dihedral : 19.104 174.347 4200 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.83 % Favored : 91.13 % Rotamer: Outliers : 4.45 % Allowed : 19.69 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.15), residues: 2718 helix: -1.17 (0.14), residues: 1351 sheet: -2.29 (0.36), residues: 187 loop : -2.76 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 378 HIS 0.005 0.001 HIS C 22 PHE 0.035 0.002 PHE I 126 TYR 0.019 0.002 TYR C 61 ARG 0.004 0.000 ARG I 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 274 time to evaluate : 2.748 Fit side-chains revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8231 (mp) REVERT: A 422 ILE cc_start: 0.9215 (tp) cc_final: 0.8945 (tt) REVERT: A 566 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: A 808 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9023 (tt) REVERT: D 113 ASP cc_start: 0.7304 (t0) cc_final: 0.6988 (t0) REVERT: D 454 LYS cc_start: 0.8422 (ttpt) cc_final: 0.7960 (mtmt) REVERT: D 471 GLU cc_start: 0.7673 (mp0) cc_final: 0.7155 (mp0) REVERT: D 493 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7511 (tm-30) REVERT: D 512 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7112 (mt-10) REVERT: E 297 ASP cc_start: 0.7098 (m-30) cc_final: 0.6214 (p0) REVERT: I 268 LYS cc_start: 0.3546 (tppt) cc_final: 0.3262 (tttp) REVERT: I 334 LEU cc_start: 0.8122 (tp) cc_final: 0.7783 (tp) REVERT: I 477 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7877 (mtpt) outliers start: 113 outliers final: 77 residues processed: 357 average time/residue: 0.3452 time to fit residues: 197.2404 Evaluate side-chains 332 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 252 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 ASN Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 92 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 273 optimal weight: 20.0000 chunk 227 optimal weight: 0.0470 chunk 126 optimal weight: 0.0030 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.8094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 178 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 GLN ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25375 Z= 0.212 Angle : 0.576 11.224 34727 Z= 0.300 Chirality : 0.042 0.176 3960 Planarity : 0.003 0.046 4013 Dihedral : 18.955 177.133 4200 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.54 % Favored : 92.42 % Rotamer: Outliers : 4.13 % Allowed : 20.31 % Favored : 75.55 % 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: -2.66 (0.15), residues: 2718 helix: -0.95 (0.14), residues: 1358 sheet: -2.21 (0.36), residues: 186 loop : -2.65 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 378 HIS 0.006 0.001 HIS C 22 PHE 0.032 0.001 PHE A 880 TYR 0.027 0.001 TYR I 291 ARG 0.006 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 281 time to evaluate : 2.690 Fit side-chains REVERT: A 357 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8216 (mp) REVERT: A 382 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6921 (mt) REVERT: A 422 ILE cc_start: 0.9199 (tp) cc_final: 0.8949 (tt) REVERT: A 566 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: A 794 MET cc_start: 0.7636 (mtm) cc_final: 0.7209 (mtm) REVERT: A 808 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8990 (tt) REVERT: B 341 SER cc_start: 0.8950 (OUTLIER) cc_final: 0.8461 (t) REVERT: B 380 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7535 (t) REVERT: C 412 PHE cc_start: 0.6942 (t80) cc_final: 0.6602 (t80) REVERT: D 113 ASP cc_start: 0.7255 (t0) cc_final: 0.6919 (t0) REVERT: D 454 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7937 (mtmt) REVERT: D 471 GLU cc_start: 0.7605 (mp0) cc_final: 0.7106 (mp0) REVERT: D 493 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7501 (tm-30) REVERT: D 512 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7042 (mt-10) REVERT: E 171 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8471 (tt) REVERT: E 297 ASP cc_start: 0.7024 (m-30) cc_final: 0.6177 (p0) REVERT: F 296 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7401 (ptp-110) REVERT: I 268 LYS cc_start: 0.3377 (tppt) cc_final: 0.3152 (tttp) REVERT: I 334 LEU cc_start: 0.8073 (tp) cc_final: 0.7770 (tp) REVERT: I 434 ASP cc_start: 0.5125 (OUTLIER) cc_final: 0.4901 (t0) REVERT: I 477 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7919 (mtpt) outliers start: 105 outliers final: 72 residues processed: 357 average time/residue: 0.3311 time to fit residues: 191.0250 Evaluate side-chains 335 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 255 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 482 ASN Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 263 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 156 optimal weight: 0.0470 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 230 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 272 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 178 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 GLN I 263 ASN I 313 GLN ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25375 Z= 0.223 Angle : 0.581 11.477 34727 Z= 0.300 Chirality : 0.042 0.166 3960 Planarity : 0.003 0.045 4013 Dihedral : 18.870 177.041 4200 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.80 % Favored : 92.16 % Rotamer: Outliers : 3.98 % Allowed : 21.18 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.16), residues: 2718 helix: -0.84 (0.14), residues: 1356 sheet: -2.20 (0.37), residues: 185 loop : -2.52 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 378 HIS 0.005 0.001 HIS C 22 PHE 0.030 0.001 PHE A 880 TYR 0.048 0.001 TYR C 23 ARG 0.006 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 277 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6935 (mt) REVERT: A 422 ILE cc_start: 0.9196 (tp) cc_final: 0.8944 (tt) REVERT: A 566 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: A 808 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8952 (tt) REVERT: B 341 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8463 (t) REVERT: B 380 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7534 (t) REVERT: C 412 PHE cc_start: 0.6984 (t80) cc_final: 0.6588 (t80) REVERT: D 113 ASP cc_start: 0.7287 (t0) cc_final: 0.6941 (t0) REVERT: D 454 LYS cc_start: 0.8404 (ttpt) cc_final: 0.7922 (mtmt) REVERT: D 471 GLU cc_start: 0.7579 (mp0) cc_final: 0.7095 (mp0) REVERT: D 493 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7497 (tm-30) REVERT: D 512 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7087 (mt-10) REVERT: E 171 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8519 (tt) REVERT: E 297 ASP cc_start: 0.7021 (m-30) cc_final: 0.6135 (p0) REVERT: F 296 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7389 (ptp-110) REVERT: I 87 GLN cc_start: 0.4142 (tm-30) cc_final: 0.3708 (mt0) REVERT: I 268 LYS cc_start: 0.3461 (tppt) cc_final: 0.3158 (tptm) REVERT: I 334 LEU cc_start: 0.8030 (tp) cc_final: 0.7762 (tp) REVERT: I 477 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7856 (mtpt) outliers start: 101 outliers final: 77 residues processed: 353 average time/residue: 0.3487 time to fit residues: 197.3173 Evaluate side-chains 349 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 266 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 ASN Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 415 ASP Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 168 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.0060 chunk 173 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 178 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 GLN ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25375 Z= 0.242 Angle : 0.596 11.846 34727 Z= 0.307 Chirality : 0.042 0.261 3960 Planarity : 0.003 0.046 4013 Dihedral : 18.848 176.979 4200 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.87 % Favored : 92.09 % Rotamer: Outliers : 4.33 % Allowed : 21.26 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2718 helix: -0.77 (0.14), residues: 1350 sheet: -2.23 (0.36), residues: 185 loop : -2.47 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 378 HIS 0.005 0.001 HIS C 22 PHE 0.032 0.001 PHE A 880 TYR 0.038 0.002 TYR C 23 ARG 0.005 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 268 time to evaluate : 2.910 Fit side-chains revert: symmetry clash REVERT: A 382 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6942 (mt) REVERT: A 422 ILE cc_start: 0.9200 (tp) cc_final: 0.8943 (tt) REVERT: A 564 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7608 (tt) REVERT: A 566 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: A 808 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9012 (tt) REVERT: B 341 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8464 (t) REVERT: B 380 THR cc_start: 0.7823 (OUTLIER) cc_final: 0.7551 (t) REVERT: C 412 PHE cc_start: 0.7013 (t80) cc_final: 0.6674 (t80) REVERT: D 113 ASP cc_start: 0.7317 (t0) cc_final: 0.6957 (t0) REVERT: D 454 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7921 (mtmt) REVERT: D 471 GLU cc_start: 0.7561 (mp0) cc_final: 0.7091 (mp0) REVERT: D 493 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7500 (tm-30) REVERT: D 512 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7069 (mt-10) REVERT: E 171 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8546 (tt) REVERT: E 291 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7705 (pp) REVERT: E 297 ASP cc_start: 0.6995 (m-30) cc_final: 0.6131 (p0) REVERT: E 411 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6337 (tm-30) REVERT: F 296 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7388 (ptp-110) REVERT: I 87 GLN cc_start: 0.4211 (tm-30) cc_final: 0.3772 (mt0) REVERT: I 334 LEU cc_start: 0.8045 (tp) cc_final: 0.7808 (tp) REVERT: I 477 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7840 (mtpt) REVERT: I 499 TYR cc_start: 0.2957 (OUTLIER) cc_final: 0.1614 (m-10) outliers start: 110 outliers final: 81 residues processed: 349 average time/residue: 0.3292 time to fit residues: 185.5899 Evaluate side-chains 348 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 258 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 ASN Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 322 TYR Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 499 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 248 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 229 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 253 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 178 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 GLN ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25375 Z= 0.172 Angle : 0.572 12.122 34727 Z= 0.295 Chirality : 0.041 0.282 3960 Planarity : 0.003 0.045 4013 Dihedral : 18.690 178.622 4198 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.43 % Favored : 92.53 % Rotamer: Outliers : 3.98 % Allowed : 21.69 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.16), residues: 2718 helix: -0.59 (0.14), residues: 1341 sheet: -2.21 (0.35), residues: 201 loop : -2.33 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 378 HIS 0.005 0.001 HIS C 22 PHE 0.028 0.001 PHE A 880 TYR 0.034 0.001 TYR C 23 ARG 0.005 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 277 time to evaluate : 2.900 Fit side-chains revert: symmetry clash REVERT: A 382 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6917 (mt) REVERT: A 422 ILE cc_start: 0.9196 (tp) cc_final: 0.8939 (tt) REVERT: A 564 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7576 (tt) REVERT: A 566 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: A 808 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8922 (tt) REVERT: B 341 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 380 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7518 (t) REVERT: C 421 ASN cc_start: 0.7829 (t0) cc_final: 0.7597 (p0) REVERT: D 113 ASP cc_start: 0.7246 (t0) cc_final: 0.6886 (t0) REVERT: D 454 LYS cc_start: 0.8378 (ttpt) cc_final: 0.7887 (mttt) REVERT: D 471 GLU cc_start: 0.7480 (mp0) cc_final: 0.6995 (mp0) REVERT: D 493 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7577 (tm-30) REVERT: D 512 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7033 (mt-10) REVERT: E 171 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8524 (tt) REVERT: E 291 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7689 (pp) REVERT: E 297 ASP cc_start: 0.6980 (m-30) cc_final: 0.6128 (p0) REVERT: E 411 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6263 (tm-30) REVERT: F 296 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7417 (ptp-110) REVERT: I 87 GLN cc_start: 0.4064 (tm-30) cc_final: 0.3642 (mt0) REVERT: I 334 LEU cc_start: 0.7987 (tp) cc_final: 0.7712 (tp) REVERT: I 499 TYR cc_start: 0.2809 (OUTLIER) cc_final: 0.1496 (m-10) outliers start: 101 outliers final: 75 residues processed: 350 average time/residue: 0.3474 time to fit residues: 194.7292 Evaluate side-chains 344 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 260 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 322 TYR Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 499 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 7.9990 chunk 268 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 281 optimal weight: 8.9990 chunk 259 optimal weight: 0.5980 chunk 224 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 178 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 25375 Z= 0.273 Angle : 0.774 59.200 34727 Z= 0.446 Chirality : 0.042 0.468 3960 Planarity : 0.004 0.142 4013 Dihedral : 18.688 178.584 4198 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.32 % Favored : 92.64 % Rotamer: Outliers : 3.62 % Allowed : 22.24 % Favored : 74.13 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2718 helix: -0.60 (0.14), residues: 1345 sheet: -2.20 (0.35), residues: 201 loop : -2.34 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 378 HIS 0.005 0.001 HIS C 22 PHE 0.028 0.001 PHE A 880 TYR 0.032 0.001 TYR C 23 ARG 0.004 0.000 ARG D 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 262 time to evaluate : 2.651 Fit side-chains revert: symmetry clash REVERT: A 382 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6919 (mt) REVERT: A 422 ILE cc_start: 0.9194 (tp) cc_final: 0.8941 (tt) REVERT: A 564 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7586 (tt) REVERT: A 566 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7219 (m-30) REVERT: A 808 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8921 (tt) REVERT: B 341 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8459 (t) REVERT: B 380 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7522 (t) REVERT: C 178 ASN cc_start: 0.4954 (OUTLIER) cc_final: 0.4283 (p0) REVERT: C 421 ASN cc_start: 0.7836 (t0) cc_final: 0.7599 (p0) REVERT: D 113 ASP cc_start: 0.7248 (t0) cc_final: 0.6892 (t0) REVERT: D 454 LYS cc_start: 0.8387 (ttpt) cc_final: 0.7885 (mttt) REVERT: D 471 GLU cc_start: 0.7478 (mp0) cc_final: 0.7004 (mp0) REVERT: D 493 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 512 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7018 (mt-10) REVERT: E 171 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8528 (tt) REVERT: E 291 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7689 (pp) REVERT: E 297 ASP cc_start: 0.6981 (m-30) cc_final: 0.6099 (p0) REVERT: E 411 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6265 (tm-30) REVERT: F 296 ARG cc_start: 0.7682 (mtp85) cc_final: 0.7417 (ptp-110) REVERT: I 87 GLN cc_start: 0.4021 (tm-30) cc_final: 0.3640 (mt0) REVERT: I 334 LEU cc_start: 0.7992 (tp) cc_final: 0.7732 (tp) REVERT: I 499 TYR cc_start: 0.2810 (OUTLIER) cc_final: 0.1496 (m-10) outliers start: 92 outliers final: 78 residues processed: 328 average time/residue: 0.3386 time to fit residues: 178.8665 Evaluate side-chains 344 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 256 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 ASN Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 322 TYR Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 499 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 178 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 28 optimal weight: 0.0030 chunk 41 optimal weight: 0.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 388 ASN ** 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 = 0.4010 r_free = 0.4010 target = 0.161278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127067 restraints weight = 35932.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127009 restraints weight = 31541.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127862 restraints weight = 32424.284| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 25375 Z= 0.273 Angle : 0.774 59.200 34727 Z= 0.446 Chirality : 0.042 0.468 3960 Planarity : 0.004 0.142 4013 Dihedral : 18.688 178.584 4198 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.32 % Favored : 92.64 % Rotamer: Outliers : 3.50 % Allowed : 22.44 % Favored : 74.06 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2718 helix: -0.60 (0.14), residues: 1345 sheet: -2.20 (0.35), residues: 201 loop : -2.34 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 378 HIS 0.005 0.001 HIS C 22 PHE 0.028 0.001 PHE A 880 TYR 0.032 0.001 TYR C 23 ARG 0.004 0.000 ARG D 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4840.18 seconds wall clock time: 89 minutes 15.33 seconds (5355.33 seconds total)