Starting phenix.real_space_refine (version: dev) on Thu Feb 23 00:26:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2023/6t8g_10400_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2023/6t8g_10400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2023/6t8g_10400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2023/6t8g_10400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2023/6t8g_10400_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2023/6t8g_10400_updated.pdb" } resolution = 4.34 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 "E ARG 632": "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: 18875 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3028 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 368} Chain breaks: 1 Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2976 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Chain breaks: 1 Chain: "C" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3013 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 368} Chain breaks: 1 Chain: "D" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2991 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain breaks: 1 Chain: "E" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3028 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 368} Chain breaks: 1 Chain: "F" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3021 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 368} Chain breaks: 1 Chain: "G" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.40, per 1000 atoms: 0.55 Number of scatterers: 18875 At special positions: 0 Unit cell: (139.384, 104.8, 135.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 44 15.00 O 3609 8.00 N 3262 7.00 C 11870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.88 Conformation dependent library (CDL) restraints added in 2.9 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 20 sheets defined 34.2% alpha, 12.5% beta 16 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 333 through 349 removed outlier: 3.849A pdb=" N MET A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 430 through 433 No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 504 through 507 removed outlier: 3.892A pdb=" N TYR A 507 " --> pdb=" O LEU A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 521 through 545 removed outlier: 4.835A pdb=" N ASN A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.820A pdb=" N LYS A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.566A pdb=" N ALA A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 643 No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 669 through 671 No H-bonds generated for 'chain 'A' and resid 669 through 671' Processing helix chain 'A' and resid 698 through 710 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 336 through 349 Processing helix chain 'B' and resid 379 through 382 No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 385 through 391 Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 430 through 433 No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 472 through 486 removed outlier: 4.095A pdb=" N LYS B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 522 through 545 removed outlier: 3.609A pdb=" N ARG B 529 " --> pdb=" O ALA B 525 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 543 " --> pdb=" O TYR B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 561 Processing helix chain 'B' and resid 598 through 603 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'B' and resid 640 through 643 No H-bonds generated for 'chain 'B' and resid 640 through 643' Processing helix chain 'B' and resid 658 through 662 removed outlier: 3.775A pdb=" N THR B 662 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 710 Processing helix chain 'C' and resid 333 through 348 Processing helix chain 'C' and resid 379 through 391 removed outlier: 5.187A pdb=" N LEU C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 385 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASP C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 521 through 543 removed outlier: 4.183A pdb=" N ASN C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 560 Processing helix chain 'C' and resid 597 through 603 Processing helix chain 'C' and resid 607 through 618 Processing helix chain 'C' and resid 657 through 663 Processing helix chain 'C' and resid 698 through 711 removed outlier: 4.250A pdb=" N GLU C 706 " --> pdb=" O HIS C 702 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 720 No H-bonds generated for 'chain 'C' and resid 718 through 720' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 333 through 349 Processing helix chain 'D' and resid 379 through 392 removed outlier: 4.446A pdb=" N LEU D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 Processing helix chain 'D' and resid 430 through 433 No H-bonds generated for 'chain 'D' and resid 430 through 433' Processing helix chain 'D' and resid 472 through 486 removed outlier: 4.211A pdb=" N LYS D 486 " --> pdb=" O SER D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 507 removed outlier: 3.668A pdb=" N TYR D 507 " --> pdb=" O LEU D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 504 through 507' Processing helix chain 'D' and resid 521 through 545 Processing helix chain 'D' and resid 550 through 563 removed outlier: 3.608A pdb=" N ALA D 563 " --> pdb=" O ASP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 603 Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 642 through 645 No H-bonds generated for 'chain 'D' and resid 642 through 645' Processing helix chain 'D' and resid 657 through 663 Processing helix chain 'D' and resid 669 through 671 No H-bonds generated for 'chain 'D' and resid 669 through 671' Processing helix chain 'D' and resid 698 through 711 Processing helix chain 'D' and resid 718 through 720 No H-bonds generated for 'chain 'D' and resid 718 through 720' Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 333 through 349 Processing helix chain 'E' and resid 379 through 391 removed outlier: 5.504A pdb=" N LYS E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP E 387 " --> pdb=" O ASN E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 430 through 433 No H-bonds generated for 'chain 'E' and resid 430 through 433' Processing helix chain 'E' and resid 472 through 483 Processing helix chain 'E' and resid 501 through 507 removed outlier: 3.699A pdb=" N SER E 505 " --> pdb=" O MET E 501 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE E 506 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR E 507 " --> pdb=" O GLU E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 501 through 507' Processing helix chain 'E' and resid 523 through 545 Processing helix chain 'E' and resid 550 through 563 removed outlier: 3.943A pdb=" N ALA E 563 " --> pdb=" O ASP E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 602 Processing helix chain 'E' and resid 606 through 617 Processing helix chain 'E' and resid 657 through 663 Processing helix chain 'E' and resid 698 through 710 Processing helix chain 'F' and resid 318 through 320 No H-bonds generated for 'chain 'F' and resid 318 through 320' Processing helix chain 'F' and resid 333 through 348 Processing helix chain 'F' and resid 378 through 391 removed outlier: 3.864A pdb=" N LEU F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA F 385 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASP F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 427 No H-bonds generated for 'chain 'F' and resid 424 through 427' Processing helix chain 'F' and resid 430 through 433 No H-bonds generated for 'chain 'F' and resid 430 through 433' Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 522 through 545 Processing helix chain 'F' and resid 550 through 562 removed outlier: 3.578A pdb=" N ARG F 555 " --> pdb=" O ALA F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 597 through 602 Processing helix chain 'F' and resid 607 through 618 Processing helix chain 'F' and resid 640 through 644 Processing helix chain 'F' and resid 657 through 663 Processing helix chain 'F' and resid 698 through 709 Processing sheet with id= A, first strand: chain 'A' and resid 397 through 400 removed outlier: 3.584A pdb=" N ARG A 398 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 649 through 651 removed outlier: 7.124A pdb=" N ILE A 650 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 463 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N LEU A 462 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 626 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL A 464 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 628 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 590 " --> pdb=" O HIS A 625 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE A 627 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 592 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA A 629 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 594 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 678 through 681 Processing sheet with id= D, first strand: chain 'A' and resid 354 through 360 removed outlier: 6.631A pdb=" N GLU A 369 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL A 359 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG A 367 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 440 through 445 removed outlier: 3.585A pdb=" N THR A 454 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 443 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A 452 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.675A pdb=" N ILE B 411 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 398 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 444 through 446 Processing sheet with id= H, first strand: chain 'B' and resid 627 through 629 removed outlier: 6.730A pdb=" N LEU B 462 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR B 648 " --> pdb=" O LEU B 463 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 398 through 400 removed outlier: 3.677A pdb=" N ILE C 411 " --> pdb=" O PHE C 368 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 358 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN C 371 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL C 356 " --> pdb=" O GLN C 371 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 649 through 652 removed outlier: 3.501A pdb=" N LEU C 443 " --> pdb=" O ILE C 452 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE C 452 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 494 through 497 removed outlier: 6.254A pdb=" N VAL C 591 " --> pdb=" O ILE C 495 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE C 497 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C 593 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS C 625 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL C 594 " --> pdb=" O HIS C 625 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 627 " --> pdb=" O VAL C 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 397 through 400 removed outlier: 4.102A pdb=" N SER D 358 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 462 through 465 removed outlier: 7.365A pdb=" N THR D 648 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N ALA D 465 " --> pdb=" O THR D 648 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D 650 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 454 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE D 452 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 492 through 498 removed outlier: 6.052A pdb=" N THR D 589 " --> pdb=" O ARG D 493 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE D 495 " --> pdb=" O THR D 589 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 591 " --> pdb=" O ILE D 495 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE D 497 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL D 593 " --> pdb=" O ILE D 497 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N HIS D 625 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL D 594 " --> pdb=" O HIS D 625 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 627 " --> pdb=" O VAL D 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 398 through 400 removed outlier: 3.540A pdb=" N ILE E 370 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN E 371 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL E 356 " --> pdb=" O GLN E 371 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 689 through 692 removed outlier: 3.579A pdb=" N ARG E 649 " --> pdb=" O LEU E 681 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU E 463 " --> pdb=" O ILE E 650 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 440 through 445 removed outlier: 3.810A pdb=" N LEU E 443 " --> pdb=" O ILE E 452 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE E 452 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 397 through 400 removed outlier: 3.668A pdb=" N GLY F 410 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 413 " --> pdb=" O THR F 366 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 440 through 442 Processing sheet with id= T, first strand: chain 'F' and resid 690 through 692 removed outlier: 3.680A pdb=" N ARG F 649 " --> pdb=" O LEU F 681 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE F 650 " --> pdb=" O HIS F 461 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU F 463 " --> pdb=" O ILE F 650 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU F 462 " --> pdb=" O ILE F 624 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU F 626 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL F 464 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU F 628 " --> pdb=" O VAL F 464 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 590 " --> pdb=" O HIS F 625 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 627 " --> pdb=" O ILE F 590 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL F 592 " --> pdb=" O ILE F 627 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA F 629 " --> pdb=" O VAL F 592 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL F 594 " --> pdb=" O ALA F 629 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 8.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5269 1.33 - 1.45: 2768 1.45 - 1.57: 10985 1.57 - 1.69: 80 1.69 - 1.81: 174 Bond restraints: 19276 Sorted by residual: bond pdb=" C SER C 332 " pdb=" N PRO C 333 " ideal model delta sigma weight residual 1.337 1.358 -0.021 9.80e-03 1.04e+04 4.64e+00 bond pdb=" CG1 ILE D 663 " pdb=" CD1 ILE D 663 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.14e+00 bond pdb=" CG ARG D 649 " pdb=" CD ARG D 649 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" CA LYS B 329 " pdb=" C LYS B 329 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.34e-02 5.57e+03 2.56e+00 bond pdb=" CG ARG E 390 " pdb=" CD ARG E 390 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.54e+00 ... (remaining 19271 not shown) Histogram of bond angle deviations from ideal: 96.32 - 105.52: 793 105.52 - 114.73: 12198 114.73 - 123.93: 12720 123.93 - 133.13: 572 133.13 - 142.34: 30 Bond angle restraints: 26313 Sorted by residual: angle pdb=" N ILE B 615 " pdb=" CA ILE B 615 " pdb=" C ILE B 615 " ideal model delta sigma weight residual 112.17 105.43 6.74 9.50e-01 1.11e+00 5.03e+01 angle pdb=" C MET F 459 " pdb=" N PRO F 460 " pdb=" CD PRO F 460 " ideal model delta sigma weight residual 120.60 105.26 15.34 2.20e+00 2.07e-01 4.86e+01 angle pdb=" C MET F 459 " pdb=" N PRO F 460 " pdb=" CA PRO F 460 " ideal model delta sigma weight residual 127.00 142.34 -15.34 2.40e+00 1.74e-01 4.08e+01 angle pdb=" C MET B 459 " pdb=" N PRO B 460 " pdb=" CD PRO B 460 " ideal model delta sigma weight residual 120.60 106.99 13.61 2.20e+00 2.07e-01 3.83e+01 angle pdb=" C MET D 459 " pdb=" N PRO D 460 " pdb=" CD PRO D 460 " ideal model delta sigma weight residual 120.60 108.38 12.22 2.20e+00 2.07e-01 3.08e+01 ... (remaining 26308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 11581 35.89 - 71.78: 208 71.78 - 107.66: 4 107.66 - 143.55: 4 143.55 - 179.44: 3 Dihedral angle restraints: 11800 sinusoidal: 4999 harmonic: 6801 Sorted by residual: dihedral pdb=" O2A ADP D 801 " pdb=" O3A ADP D 801 " pdb=" PA ADP D 801 " pdb=" PB ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 120.56 179.44 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PA ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 96.97 -156.97 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual -60.00 83.57 -143.56 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 11797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2554 0.075 - 0.150: 532 0.150 - 0.226: 41 0.226 - 0.301: 9 0.301 - 0.376: 4 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CG LEU B 550 " pdb=" CB LEU B 550 " pdb=" CD1 LEU B 550 " pdb=" CD2 LEU B 550 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE B 452 " pdb=" CA ILE B 452 " pdb=" CG1 ILE B 452 " pdb=" CG2 ILE B 452 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE D 638 " pdb=" CA ILE D 638 " pdb=" CG1 ILE D 638 " pdb=" CG2 ILE D 638 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 3137 not shown) Planarity restraints: 3226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 459 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO B 460 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 460 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 460 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 569 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO B 570 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 632 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO C 633 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 633 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 633 " -0.034 5.00e-02 4.00e+02 ... (remaining 3223 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3170 2.76 - 3.30: 17701 3.30 - 3.83: 31977 3.83 - 4.37: 35564 4.37 - 4.90: 59221 Nonbonded interactions: 147633 Sorted by model distance: nonbonded pdb=" OG SER F 660 " pdb=" O GLN F 666 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR F 539 " pdb=" O LYS F 618 " model vdw 2.241 2.440 nonbonded pdb=" OG SER F 355 " pdb=" O GLN F 371 " model vdw 2.270 2.440 nonbonded pdb=" O ILE D 483 " pdb=" OG SER D 487 " model vdw 2.295 2.440 nonbonded pdb=" OG SER C 355 " pdb=" O GLN C 371 " model vdw 2.304 2.440 ... (remaining 147628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = chain 'B' selection = (chain 'C' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = (chain 'D' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = (chain 'E' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = (chain 'F' and (resid 315 through 570 or resid 587 through 720 or resid 801)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 90 5.16 5 C 11870 2.51 5 N 3262 2.21 5 O 3609 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: 0.910 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: 5.040 Check model and map are aligned: 0.310 Process input model: 51.840 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.008 0.069 19276 Z= 0.504 Angle : 1.121 15.339 26313 Z= 0.570 Chirality : 0.061 0.376 3140 Planarity : 0.008 0.070 3226 Dihedral : 13.122 179.437 7390 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -4.29 (0.14), residues: 2343 helix: -2.63 (0.13), residues: 873 sheet: -2.12 (0.25), residues: 394 loop : -3.29 (0.15), residues: 1076 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 635 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 636 average time/residue: 0.3446 time to fit residues: 316.7426 Evaluate side-chains 367 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.396 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 435 HIS ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN D 419 GLN D 554 ASN D 617 GLN ** F 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 19276 Z= 0.267 Angle : 0.766 10.406 26313 Z= 0.371 Chirality : 0.047 0.256 3140 Planarity : 0.006 0.062 3226 Dihedral : 14.501 162.241 2909 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -2.86 (0.16), residues: 2343 helix: -1.02 (0.16), residues: 872 sheet: -1.49 (0.26), residues: 379 loop : -2.80 (0.16), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 484 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 484 average time/residue: 0.3254 time to fit residues: 235.5898 Evaluate side-chains 324 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN C 383 ASN C 435 HIS ** C 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN E 477 ASN F 666 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 19276 Z= 0.319 Angle : 0.771 10.395 26313 Z= 0.372 Chirality : 0.047 0.209 3140 Planarity : 0.005 0.049 3226 Dihedral : 14.250 167.416 2909 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -2.27 (0.17), residues: 2343 helix: -0.49 (0.17), residues: 897 sheet: -1.15 (0.26), residues: 375 loop : -2.54 (0.18), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 427 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 429 average time/residue: 0.3140 time to fit residues: 204.9752 Evaluate side-chains 310 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 2.309 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2124 time to fit residues: 3.4884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 GLN B 671 GLN C 415 ASN C 435 HIS D 419 GLN D 666 GLN E 415 ASN E 617 GLN F 666 GLN F 675 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 19276 Z= 0.285 Angle : 0.757 10.177 26313 Z= 0.361 Chirality : 0.047 0.262 3140 Planarity : 0.005 0.055 3226 Dihedral : 14.040 173.306 2909 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.17), residues: 2343 helix: -0.21 (0.18), residues: 908 sheet: -1.02 (0.27), residues: 371 loop : -2.33 (0.18), residues: 1064 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 425 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 426 average time/residue: 0.3170 time to fit residues: 204.4129 Evaluate side-chains 309 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 2.282 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 3 optimal weight: 0.0670 chunk 169 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN D 419 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 ASN F 617 GLN F 645 ASN F 666 GLN F 675 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19276 Z= 0.175 Angle : 0.700 10.122 26313 Z= 0.329 Chirality : 0.046 0.217 3140 Planarity : 0.005 0.048 3226 Dihedral : 13.598 152.649 2909 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.18), residues: 2343 helix: 0.27 (0.18), residues: 901 sheet: -0.74 (0.27), residues: 381 loop : -2.18 (0.18), residues: 1061 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.3218 time to fit residues: 215.6602 Evaluate side-chains 311 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 7.9990 chunk 205 optimal weight: 0.0670 chunk 45 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 GLN ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS C 645 ASN D 419 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN D 666 GLN F 617 GLN F 666 GLN F 675 HIS F 702 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 19276 Z= 0.286 Angle : 0.749 10.980 26313 Z= 0.357 Chirality : 0.047 0.214 3140 Planarity : 0.005 0.050 3226 Dihedral : 13.465 146.350 2909 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2343 helix: 0.24 (0.18), residues: 905 sheet: -0.64 (0.27), residues: 367 loop : -2.06 (0.18), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.3006 time to fit residues: 185.7624 Evaluate side-chains 299 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 166 optimal weight: 0.3980 chunk 129 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN D 461 HIS D 645 ASN F 617 GLN F 666 GLN F 675 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19276 Z= 0.183 Angle : 0.700 10.631 26313 Z= 0.329 Chirality : 0.046 0.194 3140 Planarity : 0.005 0.047 3226 Dihedral : 13.203 145.825 2909 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.18), residues: 2343 helix: 0.55 (0.19), residues: 889 sheet: -0.40 (0.28), residues: 373 loop : -1.92 (0.18), residues: 1081 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.3058 time to fit residues: 200.2124 Evaluate side-chains 312 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN F 360 HIS F 617 GLN F 645 ASN F 666 GLN F 675 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 19276 Z= 0.271 Angle : 0.740 11.233 26313 Z= 0.351 Chirality : 0.047 0.202 3140 Planarity : 0.005 0.055 3226 Dihedral : 13.146 137.629 2909 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.18), residues: 2343 helix: 0.45 (0.18), residues: 889 sheet: -0.37 (0.28), residues: 372 loop : -1.83 (0.19), residues: 1082 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.3127 time to fit residues: 192.2117 Evaluate side-chains 296 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 2.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 224 optimal weight: 0.4980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS D 419 GLN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN D 666 GLN E 477 ASN E 526 ASN F 617 GLN ** F 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 GLN F 675 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19276 Z= 0.210 Angle : 0.719 11.528 26313 Z= 0.338 Chirality : 0.047 0.293 3140 Planarity : 0.005 0.050 3226 Dihedral : 13.014 139.649 2909 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.92 (0.18), residues: 2343 helix: 0.50 (0.18), residues: 897 sheet: -0.24 (0.28), residues: 368 loop : -1.72 (0.19), residues: 1078 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.3148 time to fit residues: 196.8628 Evaluate side-chains 299 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.391 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 155 optimal weight: 30.0000 chunk 235 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 187 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 199 optimal weight: 0.0770 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 ASN ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN F 617 GLN ** F 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 GLN F 675 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19276 Z= 0.208 Angle : 0.736 12.360 26313 Z= 0.343 Chirality : 0.047 0.258 3140 Planarity : 0.005 0.051 3226 Dihedral : 12.915 138.846 2909 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.91 (0.18), residues: 2343 helix: 0.53 (0.19), residues: 891 sheet: -0.23 (0.28), residues: 379 loop : -1.74 (0.19), residues: 1073 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.3197 time to fit residues: 197.7732 Evaluate side-chains 305 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.0770 chunk 187 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN D 666 GLN F 617 GLN ** F 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 ASN F 675 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074874 restraints weight = 57108.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.076644 restraints weight = 37161.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.077875 restraints weight = 26913.018| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19276 Z= 0.224 Angle : 0.749 12.068 26313 Z= 0.348 Chirality : 0.047 0.250 3140 Planarity : 0.005 0.051 3226 Dihedral : 12.873 138.873 2909 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.84 (0.18), residues: 2343 helix: 0.54 (0.19), residues: 893 sheet: -0.04 (0.28), residues: 359 loop : -1.70 (0.19), residues: 1091 =============================================================================== Job complete usr+sys time: 4102.77 seconds wall clock time: 74 minutes 53.65 seconds (4493.65 seconds total)