Starting phenix.real_space_refine (version: dev) on Fri Feb 24 07:17:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zr1_6941/02_2023/5zr1_6941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zr1_6941/02_2023/5zr1_6941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zr1_6941/02_2023/5zr1_6941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zr1_6941/02_2023/5zr1_6941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zr1_6941/02_2023/5zr1_6941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zr1_6941/02_2023/5zr1_6941_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.010 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 ARG 452": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 683": "NH1" <-> "NH2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 912": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 433": "NH1" <-> "NH2" Residue "B PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 178": "NH1" <-> "NH2" Residue "E PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 272": "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 "F ARG 287": "NH1" <-> "NH2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 380": "NH1" <-> "NH2" Residue "F ARG 385": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 22260 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3958 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 484} Chain breaks: 3 Chain: "B" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3041 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "C" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4822 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 566} 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: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3758 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1335 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 831 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "A" 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: "D" 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: "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} Time building chain proxies: 11.99, per 1000 atoms: 0.54 Number of scatterers: 22260 At special positions: 0 Unit cell: (110.46, 129.396, 181.996, 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 94 16.00 P 90 15.00 Mg 3 11.99 O 4329 8.00 N 3732 7.00 C 14012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.52 Conformation dependent library (CDL) restraints added in 3.4 seconds 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4862 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 11 sheets defined 49.0% alpha, 6.7% beta 41 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 7.23 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 422 through 429 removed outlier: 3.874A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 removed outlier: 3.572A pdb=" N LEU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 501 Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.677A pdb=" N CYS A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 525 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 527 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 530 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 532 " --> pdb=" O TRP A 529 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 533 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 551 removed outlier: 4.029A pdb=" N GLU A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 579 through 587 removed outlier: 3.516A pdb=" N PHE A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 686 through 697 removed outlier: 3.548A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 725 removed outlier: 3.547A pdb=" N HIS A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 725 " --> pdb=" O TYR A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 removed outlier: 3.685A pdb=" N GLU A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 796 removed outlier: 3.897A pdb=" N ARG A 796 " --> pdb=" O THR A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 814 Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 840 through 845 removed outlier: 3.920A pdb=" N GLU A 844 " --> pdb=" O LYS A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 850 No H-bonds generated for 'chain 'A' and resid 847 through 850' Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 898 through 905 removed outlier: 3.641A pdb=" N ALA A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.778A pdb=" N ASN A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.788A pdb=" N GLU B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 331 removed outlier: 3.523A pdb=" N GLU B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.602A pdb=" N ALA B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.543A pdb=" N ASP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 411 removed outlier: 3.572A pdb=" N ASP B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 445 Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 507 through 516 removed outlier: 3.565A pdb=" N TYR B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 539 removed outlier: 3.568A pdb=" N MET B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.680A pdb=" N HIS B 561 " --> pdb=" O LYS B 557 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 4.334A pdb=" N GLU B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 615 Processing helix chain 'C' and resid 51 through 91 removed outlier: 3.510A pdb=" N LEU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.709A 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 192 through 195 No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.779A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 248 No H-bonds generated for 'chain 'C' and resid 245 through 248' Processing helix chain 'C' and resid 253 through 256 No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 277 through 287 removed outlier: 3.529A pdb=" N THR C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.650A pdb=" N PHE C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 331 removed outlier: 3.568A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.886A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 345 removed outlier: 4.209A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 353 Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 402 through 415 removed outlier: 3.608A pdb=" N LYS C 407 " --> pdb=" O ASN C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 Processing helix chain 'C' and resid 436 through 442 removed outlier: 5.432A pdb=" N ARG C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 478 No H-bonds generated for 'chain 'C' and resid 475 through 478' Processing helix chain 'C' and resid 483 through 492 removed outlier: 3.559A pdb=" N ASN C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 514 No H-bonds generated for 'chain 'C' and resid 511 through 514' Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.791A pdb=" N LYS C 526 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 547 removed outlier: 4.037A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.528A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 571 removed outlier: 3.620A pdb=" N LEU C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 585 removed outlier: 3.590A pdb=" N LEU C 581 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 593 removed outlier: 3.808A pdb=" N GLU C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 58 removed outlier: 3.686A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.630A pdb=" N GLN D 76 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP D 77 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS D 78 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN D 80 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP D 83 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 84 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 86 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 141 through 157 removed outlier: 3.726A pdb=" N GLN D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 removed outlier: 3.519A pdb=" N ILE D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 222 No H-bonds generated for 'chain 'D' and resid 219 through 222' Processing helix chain 'D' and resid 230 through 240 removed outlier: 3.583A pdb=" N GLU D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 302 through 314 Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.618A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 351 through 360 removed outlier: 3.852A pdb=" N ILE D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS D 359 " --> pdb=" O CYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 372 removed outlier: 3.585A pdb=" N ILE D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 382 removed outlier: 3.674A pdb=" N SER D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 removed outlier: 3.530A pdb=" N LEU D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 425 removed outlier: 3.656A pdb=" N ARG D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 465 removed outlier: 3.860A pdb=" N LYS D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 489 removed outlier: 3.537A pdb=" N ASN D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 496 No H-bonds generated for 'chain 'D' and resid 493 through 496' 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 516 removed outlier: 3.911A pdb=" N ARG D 515 " --> pdb=" O GLN D 511 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 526 No H-bonds generated for 'chain 'D' and resid 524 through 526' Processing helix chain 'E' and resid 12 through 21 removed outlier: 3.544A pdb=" N ASN E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 70 through 88 removed outlier: 3.850A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 87 " --> pdb=" O TYR E 83 " (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 119 removed outlier: 3.643A pdb=" N VAL E 109 " --> pdb=" O PRO E 105 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.216A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 182 removed outlier: 3.826A pdb=" N SER E 180 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR E 181 " --> pdb=" O ARG E 178 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS E 182 " --> pdb=" O TYR E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 205 Processing helix chain 'E' and resid 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 213 through 221 removed outlier: 3.803A pdb=" N ILE E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 251 removed outlier: 6.104A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 263 removed outlier: 3.716A pdb=" N ASP E 263 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 272 removed outlier: 3.773A pdb=" N SER E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 278 No H-bonds generated for 'chain 'E' and resid 275 through 278' Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.561A pdb=" N LYS E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) 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 removed outlier: 3.676A pdb=" N TYR E 330 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 333 " --> pdb=" O LYS E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 350 removed outlier: 3.693A pdb=" N ASP E 346 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA E 347 " --> pdb=" O ARG E 344 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE E 350 " --> pdb=" O ALA E 347 " (cutoff:3.500A) 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 393 Processing helix chain 'E' and resid 404 through 407 No H-bonds generated for 'chain 'E' and resid 404 through 407' Processing helix chain 'E' and resid 418 through 429 Processing helix chain 'E' and resid 456 through 465 removed outlier: 3.670A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 475 removed outlier: 3.678A pdb=" N SER E 475 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 290 removed outlier: 3.964A pdb=" N CYS F 289 " --> pdb=" O ILE F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 311 removed outlier: 3.593A pdb=" N LYS F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 331 removed outlier: 3.794A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 removed outlier: 4.182A pdb=" N LYS F 338 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 353 removed outlier: 4.015A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 372 removed outlier: 3.618A pdb=" N VAL F 369 " --> pdb=" O CYS F 365 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 385 Processing helix chain 'F' and resid 394 through 402 removed outlier: 4.401A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 429 removed outlier: 3.509A pdb=" N MET F 427 " --> pdb=" O LYS F 423 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 620 through 624 removed outlier: 6.617A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 657 through 659 removed outlier: 3.554A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 773 " --> pdb=" O ARG A 683 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 819 through 821 Processing sheet with id= D, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.758A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 589 through 592 Processing sheet with id= F, first strand: chain 'C' and resid 263 through 267 removed outlier: 6.684A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN C 103 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C 199 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N SER C 235 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET C 201 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ILE C 237 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR C 125 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C 202 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 127 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASN C 204 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 534 through 536 Processing sheet with id= H, first strand: chain 'D' and resid 272 through 274 removed outlier: 8.233A pdb=" N ILE D 273 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE D 99 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL D 98 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE D 247 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU D 100 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLY D 249 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL D 212 " --> pdb=" O CYS D 246 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE D 216 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 469 through 471 Processing sheet with id= J, first strand: chain 'E' and resid 185 through 189 removed outlier: 9.399A pdb=" N LEU E 33 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE E 166 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU E 35 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR E 168 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLY E 37 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N MET E 170 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N HIS E 58 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE E 131 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL E 60 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP E 133 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU E 62 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 433 through 435 661 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 7.70 Time building geometry restraints manager: 10.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 6999 1.35 - 1.50: 6994 1.50 - 1.65: 8721 1.65 - 1.80: 104 1.80 - 1.94: 51 Bond restraints: 22869 Sorted by residual: bond pdb=" O2A AGS A2001 " pdb=" PA AGS A2001 " ideal model delta sigma weight residual 1.531 1.465 0.066 1.60e-02 3.91e+03 1.68e+01 bond pdb=" O2B AGS E2001 " pdb=" PB AGS E2001 " ideal model delta sigma weight residual 1.531 1.466 0.065 1.60e-02 3.91e+03 1.65e+01 bond pdb=" N LYS C 603 " pdb=" CA LYS C 603 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.23e-02 6.61e+03 1.45e+01 bond pdb=" O2A AGS E2001 " pdb=" PA AGS E2001 " ideal model delta sigma weight residual 1.531 1.472 0.059 1.60e-02 3.91e+03 1.35e+01 bond pdb=" N ASP F 390 " pdb=" CA ASP F 390 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.23e+00 ... (remaining 22864 not shown) Histogram of bond angle deviations from ideal: 96.32 - 104.74: 605 104.74 - 113.16: 12444 113.16 - 121.58: 13044 121.58 - 130.00: 5024 130.00 - 138.42: 152 Bond angle restraints: 31269 Sorted by residual: angle pdb=" CA LEU D 372 " pdb=" CB LEU D 372 " pdb=" CG LEU D 372 " ideal model delta sigma weight residual 116.30 138.42 -22.12 3.50e+00 8.16e-02 3.99e+01 angle pdb=" CA GLU E 370 " pdb=" CB GLU E 370 " pdb=" CG GLU E 370 " ideal model delta sigma weight residual 114.10 126.37 -12.27 2.00e+00 2.50e-01 3.76e+01 angle pdb=" CA LYS C 603 " pdb=" CB LYS C 603 " pdb=" CG LYS C 603 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 angle pdb=" N THR B 242 " pdb=" CA THR B 242 " pdb=" C THR B 242 " ideal model delta sigma weight residual 110.80 101.07 9.73 2.13e+00 2.20e-01 2.09e+01 angle pdb=" C TYR B 473 " pdb=" N ASN B 474 " pdb=" CA ASN B 474 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 ... (remaining 31264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.81: 12829 28.81 - 57.62: 659 57.62 - 86.44: 49 86.44 - 115.25: 0 115.25 - 144.06: 2 Dihedral angle restraints: 13539 sinusoidal: 6079 harmonic: 7460 Sorted by residual: dihedral pdb=" CA LEU E 171 " pdb=" C LEU E 171 " pdb=" N GLU E 172 " pdb=" CA GLU E 172 " ideal model delta harmonic sigma weight residual -180.00 -140.93 -39.07 0 5.00e+00 4.00e-02 6.11e+01 dihedral pdb=" CA THR D 66 " pdb=" C THR D 66 " pdb=" N ASP D 67 " pdb=" CA ASP D 67 " ideal model delta harmonic sigma weight residual 180.00 141.97 38.03 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA ASP B 241 " pdb=" C ASP B 241 " pdb=" N THR B 242 " pdb=" CA THR B 242 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 13536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3257 0.098 - 0.196: 274 0.196 - 0.295: 12 0.295 - 0.393: 3 0.393 - 0.491: 1 Chirality restraints: 3547 Sorted by residual: chirality pdb=" PB AGS E2001 " pdb=" O2B AGS E2001 " pdb=" O3A AGS E2001 " pdb=" O3B AGS E2001 " both_signs ideal model delta sigma weight residual True 3.18 -2.69 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CB THR E 321 " pdb=" CA THR E 321 " pdb=" OG1 THR E 321 " pdb=" CG2 THR E 321 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ASP F 390 " pdb=" N ASP F 390 " pdb=" C ASP F 390 " pdb=" CB ASP F 390 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3544 not shown) Planarity restraints: 3651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 394 " 0.021 2.00e-02 2.50e+03 2.20e-02 8.43e+00 pdb=" CG PHE A 394 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 394 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 394 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 394 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 394 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 394 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 36 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" CD GLN E 36 " -0.050 2.00e-02 2.50e+03 pdb=" OE1 GLN E 36 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN E 36 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 371 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" C VAL E 371 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL E 371 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN E 372 " 0.016 2.00e-02 2.50e+03 ... (remaining 3648 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 197 2.62 - 3.19: 18035 3.19 - 3.76: 35293 3.76 - 4.33: 50904 4.33 - 4.90: 79611 Nonbonded interactions: 184040 Sorted by model distance: nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D2002 " model vdw 2.050 2.170 nonbonded pdb=" O2G AGS D2001 " pdb="MG MG D2002 " model vdw 2.078 2.170 nonbonded pdb=" OG1 THR A 486 " pdb="MG MG A2002 " model vdw 2.110 2.170 nonbonded pdb=" O2B AGS A2001 " pdb="MG MG A2002 " model vdw 2.128 2.170 nonbonded pdb=" O3G AGS E2001 " pdb="MG MG E2002 " model vdw 2.145 2.170 ... (remaining 184035 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 90 5.49 5 Mg 3 5.21 5 S 94 5.16 5 C 14012 2.51 5 N 3732 2.21 5 O 4329 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 5.300 Check model and map are aligned: 0.310 Process input model: 60.500 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 0.071 22869 Z= 0.411 Angle : 1.040 22.122 31269 Z= 0.541 Chirality : 0.058 0.491 3547 Planarity : 0.006 0.067 3651 Dihedral : 15.458 144.062 8677 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -5.16 (0.12), residues: 2479 helix: -4.35 (0.06), residues: 1330 sheet: -1.74 (0.32), residues: 206 loop : -1.99 (0.17), residues: 943 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 422 time to evaluate : 2.560 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 433 average time/residue: 1.4213 time to fit residues: 696.9432 Evaluate side-chains 233 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 230 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 3.2377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 581 ASN A 600 ASN A 787 ASN A 836 ASN A 895 ASN B 310 GLN B 364 ASN B 425 HIS B 426 ASN B 467 ASN B 478 HIS B 493 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 560 ASN C 53 ASN C 62 HIS C 67 HIS C 190 ASN C 214 ASN C 239 ASN C 246 ASN C 250 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN D 105 GLN D 126 GLN D 137 HIS D 140 GLN D 155 GLN D 233 ASN D 240 HIS D 279 GLN D 371 GLN D 458 ASN D 491 GLN ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN E 163 ASN E 277 ASN E 377 GLN E 391 GLN E 422 GLN E 423 ASN E 453 ASN F 318 GLN F 383 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22869 Z= 0.204 Angle : 0.630 13.992 31269 Z= 0.336 Chirality : 0.042 0.184 3547 Planarity : 0.004 0.048 3651 Dihedral : 18.050 143.150 3560 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 3.95 % 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: -3.19 (0.14), residues: 2479 helix: -2.41 (0.11), residues: 1299 sheet: -1.33 (0.32), residues: 212 loop : -1.58 (0.17), residues: 968 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 277 time to evaluate : 2.593 Fit side-chains revert: symmetry clash outliers start: 91 outliers final: 26 residues processed: 341 average time/residue: 1.1959 time to fit residues: 473.4848 Evaluate side-chains 247 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 2.509 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 8 average time/residue: 0.2930 time to fit residues: 7.1365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 0.0170 chunk 72 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 608 GLN B 493 GLN B 534 GLN B 538 ASN B 560 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 240 HIS D 462 ASN D 491 GLN D 493 GLN E 32 ASN F 318 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 22869 Z= 0.237 Angle : 0.600 10.138 31269 Z= 0.316 Chirality : 0.043 0.198 3547 Planarity : 0.004 0.045 3651 Dihedral : 18.024 153.690 3560 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 4.25 % 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: -2.03 (0.15), residues: 2479 helix: -1.23 (0.13), residues: 1314 sheet: -0.84 (0.35), residues: 200 loop : -1.40 (0.18), residues: 965 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 236 time to evaluate : 2.717 Fit side-chains revert: symmetry clash outliers start: 98 outliers final: 40 residues processed: 305 average time/residue: 1.2401 time to fit residues: 437.3019 Evaluate side-chains 254 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 214 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 31 residues processed: 10 average time/residue: 0.2871 time to fit residues: 8.1320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 234 optimal weight: 0.3980 chunk 248 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 222 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN B 467 ASN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 560 ASN C 69 HIS ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN C 332 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 240 HIS D 446 ASN D 491 GLN E 182 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 22869 Z= 0.191 Angle : 0.556 8.630 31269 Z= 0.294 Chirality : 0.042 0.229 3547 Planarity : 0.003 0.044 3651 Dihedral : 17.907 157.448 3560 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 3.78 % 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: -1.35 (0.16), residues: 2479 helix: -0.56 (0.14), residues: 1313 sheet: -0.64 (0.35), residues: 202 loop : -1.24 (0.18), residues: 964 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 242 time to evaluate : 2.679 Fit side-chains revert: symmetry clash outliers start: 87 outliers final: 38 residues processed: 300 average time/residue: 1.2567 time to fit residues: 437.1201 Evaluate side-chains 254 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 216 time to evaluate : 2.155 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 31 residues processed: 8 average time/residue: 0.3080 time to fit residues: 7.2365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 171 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 222 optimal weight: 0.0040 chunk 62 optimal weight: 2.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 608 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 550 GLN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 446 ASN D 491 GLN E 391 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 22869 Z= 0.234 Angle : 0.565 9.875 31269 Z= 0.297 Chirality : 0.042 0.230 3547 Planarity : 0.003 0.045 3651 Dihedral : 17.901 159.942 3560 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 3.82 % 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: -1.04 (0.16), residues: 2479 helix: -0.27 (0.14), residues: 1326 sheet: -0.43 (0.36), residues: 200 loop : -1.19 (0.19), residues: 953 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 228 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 52 residues processed: 285 average time/residue: 1.2618 time to fit residues: 417.7432 Evaluate side-chains 266 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 214 time to evaluate : 2.531 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 41 residues processed: 12 average time/residue: 0.3701 time to fit residues: 10.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 82 optimal weight: 0.0170 chunk 130 optimal weight: 0.8980 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 581 ASN A 608 GLN A 787 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 538 ASN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 491 GLN E 391 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 22869 Z= 0.186 Angle : 0.537 9.639 31269 Z= 0.284 Chirality : 0.041 0.219 3547 Planarity : 0.003 0.045 3651 Dihedral : 17.823 161.663 3560 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2479 helix: 0.02 (0.14), residues: 1322 sheet: -0.34 (0.36), residues: 202 loop : -1.07 (0.19), residues: 955 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 246 time to evaluate : 2.341 Fit side-chains revert: symmetry clash outliers start: 83 outliers final: 46 residues processed: 306 average time/residue: 1.2747 time to fit residues: 452.7846 Evaluate side-chains 263 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 2.704 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 40 residues processed: 7 average time/residue: 0.6081 time to fit residues: 9.3093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 0.0980 chunk 138 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 608 GLN A 787 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 538 ASN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 370 ASN D 491 GLN E 52 ASN E 391 GLN E 440 ASN E 453 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 22869 Z= 0.305 Angle : 0.594 10.684 31269 Z= 0.311 Chirality : 0.044 0.238 3547 Planarity : 0.003 0.047 3651 Dihedral : 17.934 166.843 3560 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 3.99 % 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: -0.72 (0.16), residues: 2479 helix: 0.01 (0.14), residues: 1328 sheet: -0.34 (0.37), residues: 202 loop : -1.07 (0.19), residues: 949 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 221 time to evaluate : 2.547 Fit side-chains revert: symmetry clash outliers start: 92 outliers final: 50 residues processed: 289 average time/residue: 1.2286 time to fit residues: 411.5445 Evaluate side-chains 269 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 219 time to evaluate : 2.575 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 43 residues processed: 8 average time/residue: 0.7252 time to fit residues: 10.4140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 147 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 787 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 446 ASN D 491 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN E 453 ASN F 407 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 22869 Z= 0.173 Angle : 0.528 10.010 31269 Z= 0.282 Chirality : 0.041 0.215 3547 Planarity : 0.003 0.046 3651 Dihedral : 17.771 167.209 3560 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2479 helix: 0.30 (0.15), residues: 1323 sheet: -0.30 (0.36), residues: 202 loop : -1.01 (0.19), residues: 954 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 244 time to evaluate : 2.691 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 47 residues processed: 299 average time/residue: 1.3083 time to fit residues: 455.0211 Evaluate side-chains 271 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 224 time to evaluate : 2.560 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 41 residues processed: 7 average time/residue: 0.5641 time to fit residues: 8.5828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 181 optimal weight: 0.0010 chunk 70 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 491 GLN E 277 ASN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN E 453 ASN F 309 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 22869 Z= 0.219 Angle : 0.555 9.891 31269 Z= 0.294 Chirality : 0.042 0.224 3547 Planarity : 0.003 0.046 3651 Dihedral : 17.777 169.654 3560 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2479 helix: 0.35 (0.14), residues: 1337 sheet: -0.26 (0.36), residues: 202 loop : -0.98 (0.19), residues: 940 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 233 time to evaluate : 2.953 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 40 residues processed: 289 average time/residue: 1.2203 time to fit residues: 410.0201 Evaluate side-chains 262 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 2.377 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 37 residues processed: 3 average time/residue: 0.7690 time to fit residues: 6.2350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 787 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 446 ASN D 491 GLN D 493 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN E 453 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.098 22869 Z= 0.188 Angle : 0.541 10.353 31269 Z= 0.286 Chirality : 0.041 0.203 3547 Planarity : 0.003 0.045 3651 Dihedral : 17.717 170.746 3560 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2479 helix: 0.52 (0.15), residues: 1320 sheet: -0.23 (0.36), residues: 202 loop : -0.93 (0.19), residues: 957 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 227 time to evaluate : 2.402 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 41 residues processed: 271 average time/residue: 1.3016 time to fit residues: 407.7694 Evaluate side-chains 258 residues out of total 2304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 2.465 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 3 average time/residue: 0.5761 time to fit residues: 5.6768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 85 optimal weight: 0.0020 chunk 209 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 787 ASN B 493 GLN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 491 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116547 restraints weight = 26574.280| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.11 r_work: 0.2954 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 22869 Z= 0.291 Angle : 0.594 11.337 31269 Z= 0.311 Chirality : 0.044 0.256 3547 Planarity : 0.003 0.046 3651 Dihedral : 17.853 176.283 3560 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 2.43 % 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: -0.31 (0.17), residues: 2479 helix: 0.39 (0.14), residues: 1332 sheet: -0.21 (0.36), residues: 202 loop : -0.94 (0.19), residues: 945 =============================================================================== Job complete usr+sys time: 7402.19 seconds wall clock time: 132 minutes 10.68 seconds (7930.68 seconds total)