Starting phenix.real_space_refine (version: dev) on Sat Feb 25 04:34:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2023/7mca_23755_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2023/7mca_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_2023/7mca_23755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2023/7mca_23755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2023/7mca_23755_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mca_23755/02_2023/7mca_23755_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 13.45, per 1000 atoms: 0.54 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: 10.11 Conformation dependent library (CDL) restraints added in 3.2 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: 8.43 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: 8.62 Time building geometry restraints manager: 10.91 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: 14111 33.57 - 67.14: 857 67.14 - 100.72: 43 100.72 - 134.29: 1 134.29 - 167.86: 1 Dihedral angle restraints: 15013 sinusoidal: 6812 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 15010 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.020 Extract box with map and model: 6.820 Check model and map are aligned: 0.370 Process input model: 67.310 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 19.214 167.859 9659 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 % 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 *********************** 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 : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 512 average time/residue: 0.4320 time to fit residues: 328.8262 Evaluate side-chains 271 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 266 time to evaluate : 2.760 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2864 time to fit residues: 6.1679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 327 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 124 GLN 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: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1898 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= 0.206 Angle : 0.611 12.630 34727 Z= 0.327 Chirality : 0.043 0.170 3960 Planarity : 0.004 0.058 4013 Dihedral : 19.112 171.586 4010 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 2.40 % 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: -3.82 (0.14), residues: 2718 helix: -2.16 (0.12), residues: 1364 sheet: -2.25 (0.35), residues: 197 loop : -2.96 (0.16), residues: 1157 *********************** 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 385 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 324 time to evaluate : 2.562 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 32 residues processed: 365 average time/residue: 0.3793 time to fit residues: 218.2743 Evaluate side-chains 298 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 2.757 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2463 time to fit residues: 18.0392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 174 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 278 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN 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 477 GLN C 486 ASN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN D 327 ASN D 446 ASN E 82 GLN E 139 GLN E 182 HIS E 223 GLN ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 HIS I 213 HIS I 232 ASN I 289 GLN I 313 GLN ** I 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 25375 Z= 0.422 Angle : 0.720 13.287 34727 Z= 0.373 Chirality : 0.047 0.269 3960 Planarity : 0.005 0.053 4013 Dihedral : 19.380 164.921 4010 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer Outliers : 3.23 % 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: -3.53 (0.14), residues: 2718 helix: -1.78 (0.13), residues: 1343 sheet: -2.34 (0.35), residues: 188 loop : -2.97 (0.16), residues: 1187 *********************** 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 366 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 284 time to evaluate : 2.779 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 45 residues processed: 341 average time/residue: 0.3669 time to fit residues: 199.2070 Evaluate side-chains 286 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 2.830 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2275 time to fit residues: 23.1967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 133 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 258 optimal weight: 20.0000 chunk 273 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 342 GLN B 493 GLN C 214 ASN C 239 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8037 moved from start: 0.2707 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= 0.207 Angle : 0.589 11.300 34727 Z= 0.309 Chirality : 0.042 0.182 3960 Planarity : 0.003 0.049 4013 Dihedral : 19.155 171.044 4010 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.65 % Favored : 92.31 % Rotamer Outliers : 1.57 % 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: -3.05 (0.15), residues: 2718 helix: -1.33 (0.14), residues: 1350 sheet: -2.21 (0.36), residues: 188 loop : -2.79 (0.16), residues: 1180 *********************** 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 321 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 281 time to evaluate : 2.768 Fit side-chains outliers start: 40 outliers final: 17 residues processed: 311 average time/residue: 0.4174 time to fit residues: 209.8340 Evaluate side-chains 263 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 246 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2573 time to fit residues: 11.7641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 227 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 189 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 245 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 HIS ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 GLN 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: 0.8027 moved from start: 0.2917 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= 0.212 Angle : 0.575 10.813 34727 Z= 0.300 Chirality : 0.042 0.177 3960 Planarity : 0.003 0.046 4013 Dihedral : 18.952 171.421 4010 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.02 % Favored : 91.94 % Rotamer Outliers : 1.93 % 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: -2.72 (0.15), residues: 2718 helix: -1.01 (0.14), residues: 1356 sheet: -2.17 (0.36), residues: 188 loop : -2.68 (0.16), residues: 1174 *********************** 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 337 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 288 time to evaluate : 2.902 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 25 residues processed: 318 average time/residue: 0.3797 time to fit residues: 193.4880 Evaluate side-chains 277 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 252 time to evaluate : 3.846 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2459 time to fit residues: 15.8256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 92 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 563 ASN D 319 ASN D 489 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 198 GLN I 263 ASN I 313 GLN ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.066 25375 Z= 0.421 Angle : 0.700 13.034 34727 Z= 0.360 Chirality : 0.047 0.248 3960 Planarity : 0.004 0.051 4013 Dihedral : 19.186 167.187 4010 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.71 % Favored : 90.25 % Rotamer Outliers : 2.60 % 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: -2.91 (0.15), residues: 2718 helix: -1.19 (0.14), residues: 1342 sheet: -2.30 (0.36), residues: 187 loop : -2.72 (0.16), residues: 1189 *********************** 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 326 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 260 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 35 residues processed: 310 average time/residue: 0.3635 time to fit residues: 181.3182 Evaluate side-chains 285 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 250 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2287 time to fit residues: 18.7287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 263 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 199 optimal weight: 0.9980 chunk 154 optimal weight: 40.0000 chunk 230 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 600 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN ** 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: 0.8052 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 25375 Z= 0.227 Angle : 0.593 12.637 34727 Z= 0.307 Chirality : 0.042 0.177 3960 Planarity : 0.003 0.046 4013 Dihedral : 18.938 173.050 4010 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.13 % Favored : 91.83 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.15), residues: 2718 helix: -0.92 (0.14), residues: 1340 sheet: -2.25 (0.36), residues: 187 loop : -2.57 (0.17), residues: 1191 *********************** 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 316 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 278 time to evaluate : 2.796 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 302 average time/residue: 0.3811 time to fit residues: 181.7261 Evaluate side-chains 283 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 263 time to evaluate : 2.844 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2532 time to fit residues: 13.0799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 168 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 82 optimal weight: 0.0040 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** 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** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25375 Z= 0.170 Angle : 0.572 11.756 34727 Z= 0.295 Chirality : 0.041 0.159 3960 Planarity : 0.003 0.045 4013 Dihedral : 18.684 174.480 4010 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.51 % Favored : 92.46 % Rotamer Outliers : 0.87 % 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: -2.28 (0.16), residues: 2718 helix: -0.64 (0.15), residues: 1335 sheet: -2.13 (0.37), residues: 187 loop : -2.42 (0.17), residues: 1196 *********************** 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 305 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 283 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 298 average time/residue: 0.3742 time to fit residues: 177.4166 Evaluate side-chains 272 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 2.848 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2313 time to fit residues: 8.2609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 248 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 152 optimal weight: 0.0870 chunk 110 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 253 optimal weight: 0.2980 overall best weight: 2.0762 ------------------------------------------------------------------------------- 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** ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3532 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= 0.233 Angle : 0.595 12.014 34727 Z= 0.307 Chirality : 0.042 0.184 3960 Planarity : 0.003 0.042 4013 Dihedral : 18.677 172.693 4010 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.06 % Favored : 91.91 % Rotamer Outliers : 0.91 % 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: -2.25 (0.16), residues: 2718 helix: -0.61 (0.14), residues: 1339 sheet: -2.11 (0.37), residues: 186 loop : -2.41 (0.17), residues: 1193 *********************** 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 289 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 266 time to evaluate : 3.022 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 278 average time/residue: 0.3889 time to fit residues: 171.1970 Evaluate side-chains 267 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 254 time to evaluate : 2.887 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2443 time to fit residues: 10.0415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 5.9990 chunk 268 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 127 optimal weight: 0.0870 chunk 186 optimal weight: 0.9990 chunk 281 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- 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 241 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 HIS ** 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: 0.7995 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25375 Z= 0.172 Angle : 0.578 12.587 34727 Z= 0.297 Chirality : 0.041 0.278 3960 Planarity : 0.003 0.045 4013 Dihedral : 18.479 175.740 4010 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.14 % Favored : 92.83 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.16), residues: 2718 helix: -0.45 (0.15), residues: 1334 sheet: -2.00 (0.37), residues: 185 loop : -2.31 (0.17), residues: 1199 ********************** 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 281 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 275 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 277 average time/residue: 0.3952 time to fit residues: 173.9777 Evaluate side-chains 257 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 255 time to evaluate : 3.084 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3889 time to fit residues: 5.3307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 178 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 230 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 262 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.158830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124680 restraints weight = 36256.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123789 restraints weight = 34264.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125082 restraints weight = 37097.599| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 25375 Z= 0.320 Angle : 0.645 12.493 34727 Z= 0.330 Chirality : 0.045 0.272 3960 Planarity : 0.004 0.043 4013 Dihedral : 18.684 170.628 4010 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.16 % Favored : 90.80 % Rotamer Outliers : 0.59 % 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: -2.25 (0.16), residues: 2718 helix: -0.59 (0.14), residues: 1322 sheet: -2.21 (0.37), residues: 186 loop : -2.39 (0.17), residues: 1210 =============================================================================== Job complete usr+sys time: 4504.74 seconds wall clock time: 83 minutes 51.30 seconds (5031.30 seconds total)