Starting phenix.real_space_refine on Sat Feb 17 14:02:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2024/6t8g_10400_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2024/6t8g_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_2024/6t8g_10400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2024/6t8g_10400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2024/6t8g_10400_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8g_10400/02_2024/6t8g_10400_updated.pdb" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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-5238/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: 9.85, per 1000 atoms: 0.52 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: 7.34 Conformation dependent library (CDL) restraints added in 3.3 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: 7.62 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: 5.40 Time building geometry restraints manager: 7.92 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: 11635 35.89 - 71.78: 218 71.78 - 107.66: 4 107.66 - 143.55: 4 143.55 - 179.44: 3 Dihedral angle restraints: 11864 sinusoidal: 5063 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 11861 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 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.900 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 52.410 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 13.329 179.437 7454 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 % Allowed : 5.70 % Favored : 94.15 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP A 530 HIS 0.013 0.002 HIS B 625 PHE 0.025 0.003 PHE E 597 TYR 0.030 0.003 TYR D 507 ARG 0.009 0.001 ARG D 711 *********************** 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 : 2.125 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 REVERT: A 435 HIS cc_start: 0.9094 (t-90) cc_final: 0.8235 (t-90) REVERT: A 513 LEU cc_start: 0.8782 (tt) cc_final: 0.8400 (tt) REVERT: A 517 VAL cc_start: 0.8890 (t) cc_final: 0.8368 (m) REVERT: A 521 MET cc_start: 0.7301 (pp-130) cc_final: 0.5549 (pp-130) REVERT: A 535 MET cc_start: 0.8756 (ttm) cc_final: 0.8186 (ttp) REVERT: A 602 MET cc_start: 0.9019 (mtp) cc_final: 0.8735 (mtm) REVERT: A 609 GLU cc_start: 0.8245 (tp30) cc_final: 0.7885 (tp30) REVERT: A 614 ARG cc_start: 0.8518 (tmt-80) cc_final: 0.8253 (ttp-170) REVERT: A 632 ARG cc_start: 0.8112 (ppt-90) cc_final: 0.6618 (ptt-90) REVERT: A 650 ILE cc_start: 0.9368 (mt) cc_final: 0.9099 (tt) REVERT: A 678 MET cc_start: 0.7114 (pp-130) cc_final: 0.6557 (pp-130) REVERT: A 679 LEU cc_start: 0.8641 (mm) cc_final: 0.8278 (mm) REVERT: A 695 PHE cc_start: 0.8741 (t80) cc_final: 0.8446 (t80) REVERT: A 699 ASP cc_start: 0.9214 (m-30) cc_final: 0.8903 (t70) REVERT: B 445 HIS cc_start: 0.8335 (m90) cc_final: 0.8005 (m-70) REVERT: B 519 THR cc_start: 0.8761 (m) cc_final: 0.8528 (p) REVERT: B 542 MET cc_start: 0.9140 (ttp) cc_final: 0.8726 (ttp) REVERT: B 556 LYS cc_start: 0.9404 (mmpt) cc_final: 0.8950 (ptmm) REVERT: B 600 MET cc_start: 0.8213 (mtp) cc_final: 0.7787 (mtp) REVERT: B 614 ARG cc_start: 0.7583 (mpp80) cc_final: 0.6956 (mmm-85) REVERT: B 632 ARG cc_start: 0.5755 (tmm160) cc_final: 0.5548 (tmm160) REVERT: B 699 ASP cc_start: 0.8901 (m-30) cc_final: 0.8583 (t70) REVERT: B 716 TYR cc_start: 0.8375 (m-80) cc_final: 0.8174 (m-80) REVERT: C 425 GLU cc_start: 0.9199 (tt0) cc_final: 0.8555 (tm-30) REVERT: C 507 TYR cc_start: 0.8676 (m-80) cc_final: 0.8222 (m-80) REVERT: C 631 GLN cc_start: 0.8859 (tt0) cc_final: 0.7665 (tt0) REVERT: D 318 LEU cc_start: 0.9232 (tp) cc_final: 0.8980 (mp) REVERT: D 406 LYS cc_start: 0.8984 (mttt) cc_final: 0.8642 (mtpm) REVERT: D 441 LEU cc_start: 0.9092 (mt) cc_final: 0.8827 (mt) REVERT: D 468 THR cc_start: 0.8502 (p) cc_final: 0.7816 (m) REVERT: D 479 MET cc_start: 0.9340 (mtt) cc_final: 0.8873 (mtm) REVERT: D 595 ASP cc_start: 0.8269 (t0) cc_final: 0.8042 (t0) REVERT: D 632 ARG cc_start: 0.8534 (ptt180) cc_final: 0.7891 (tpp-160) REVERT: D 641 LEU cc_start: 0.9086 (tp) cc_final: 0.8595 (mp) REVERT: D 708 TRP cc_start: 0.8608 (m100) cc_final: 0.7962 (m100) REVERT: E 459 MET cc_start: 0.9150 (mtp) cc_final: 0.8375 (mtp) REVERT: E 540 ARG cc_start: 0.8542 (mtt180) cc_final: 0.7812 (mtm-85) REVERT: E 591 VAL cc_start: 0.9614 (t) cc_final: 0.9350 (m) REVERT: E 600 MET cc_start: 0.8778 (mtt) cc_final: 0.8545 (mtt) REVERT: E 675 HIS cc_start: 0.8044 (m170) cc_final: 0.7641 (m-70) REVERT: E 678 MET cc_start: 0.8659 (mtm) cc_final: 0.8418 (mtm) REVERT: E 702 HIS cc_start: 0.8719 (m90) cc_final: 0.8155 (m90) REVERT: F 339 MET cc_start: 0.9423 (tpp) cc_final: 0.9154 (tpp) REVERT: F 368 PHE cc_start: 0.9449 (m-80) cc_final: 0.9107 (m-10) REVERT: F 371 GLN cc_start: 0.9063 (tt0) cc_final: 0.8540 (tm-30) REVERT: F 431 GLU cc_start: 0.8745 (pm20) cc_final: 0.8232 (pm20) REVERT: F 601 MET cc_start: 0.7814 (tmt) cc_final: 0.6844 (tmm) REVERT: F 633 PRO cc_start: 0.8593 (Cg_exo) cc_final: 0.7505 (Cg_endo) REVERT: F 659 ASP cc_start: 0.7478 (m-30) cc_final: 0.7122 (m-30) outliers start: 3 outliers final: 0 residues processed: 636 average time/residue: 0.3406 time to fit residues: 313.9894 Evaluate side-chains 376 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.105 ------------------------------------------------------------------------------- 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: 3.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 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 445 HIS ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN C 631 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2585 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= 0.270 Angle : 0.758 10.465 26313 Z= 0.368 Chirality : 0.047 0.253 3140 Planarity : 0.006 0.056 3226 Dihedral : 14.800 162.228 2973 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % 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: -1.03 (0.16), residues: 868 sheet: -1.57 (0.26), residues: 389 loop : -2.76 (0.16), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 530 HIS 0.009 0.001 HIS B 625 PHE 0.011 0.001 PHE A 553 TYR 0.032 0.002 TYR E 432 ARG 0.008 0.001 ARG B 529 *********************** 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 482 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 480 time to evaluate : 2.014 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: A 435 HIS cc_start: 0.8889 (t-90) cc_final: 0.8334 (t-90) REVERT: A 481 LEU cc_start: 0.9759 (mm) cc_final: 0.9519 (mm) REVERT: A 595 ASP cc_start: 0.7482 (t70) cc_final: 0.7144 (t70) REVERT: A 609 GLU cc_start: 0.8208 (tp30) cc_final: 0.7809 (tp30) REVERT: A 626 LEU cc_start: 0.9689 (tp) cc_final: 0.9454 (tp) REVERT: A 675 HIS cc_start: 0.7640 (m170) cc_final: 0.7290 (m170) REVERT: A 678 MET cc_start: 0.7714 (ptt) cc_final: 0.7444 (ptm) REVERT: A 699 ASP cc_start: 0.9126 (m-30) cc_final: 0.8803 (t70) REVERT: B 419 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 432 TYR cc_start: 0.9371 (t80) cc_final: 0.9002 (t80) REVERT: B 445 HIS cc_start: 0.8610 (m-70) cc_final: 0.7872 (m-70) REVERT: B 447 ILE cc_start: 0.8152 (mm) cc_final: 0.7861 (mm) REVERT: B 529 ARG cc_start: 0.8545 (mpp-170) cc_final: 0.8162 (mtt-85) REVERT: B 535 MET cc_start: 0.9287 (tmm) cc_final: 0.8979 (tmm) REVERT: B 542 MET cc_start: 0.9154 (ttp) cc_final: 0.8708 (ttp) REVERT: B 556 LYS cc_start: 0.9355 (mmpt) cc_final: 0.8980 (pttp) REVERT: B 632 ARG cc_start: 0.5251 (tmm160) cc_final: 0.5012 (tmm160) REVERT: B 664 LEU cc_start: 0.7099 (tp) cc_final: 0.6617 (tp) REVERT: B 699 ASP cc_start: 0.8910 (m-30) cc_final: 0.8662 (t70) REVERT: C 425 GLU cc_start: 0.9269 (tt0) cc_final: 0.8480 (tm-30) REVERT: C 507 TYR cc_start: 0.8708 (m-80) cc_final: 0.8265 (m-80) REVERT: C 521 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6537 (mmm) REVERT: C 666 GLN cc_start: 0.6633 (mp10) cc_final: 0.6278 (mp10) REVERT: D 318 LEU cc_start: 0.9332 (tp) cc_final: 0.9085 (mp) REVERT: D 369 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6943 (tt0) REVERT: D 406 LYS cc_start: 0.9035 (mttt) cc_final: 0.8352 (mtpt) REVERT: D 441 LEU cc_start: 0.9079 (mt) cc_final: 0.8646 (mt) REVERT: D 447 ILE cc_start: 0.9539 (pt) cc_final: 0.9201 (mp) REVERT: D 479 MET cc_start: 0.9277 (mtt) cc_final: 0.8637 (mtm) REVERT: D 595 ASP cc_start: 0.8207 (t0) cc_final: 0.7869 (t0) REVERT: D 602 MET cc_start: 0.8344 (tpt) cc_final: 0.8001 (tmm) REVERT: D 610 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8457 (pp20) REVERT: D 632 ARG cc_start: 0.8354 (ptt180) cc_final: 0.7848 (tpm170) REVERT: E 369 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7353 (mt-10) REVERT: E 459 MET cc_start: 0.9219 (mtp) cc_final: 0.8485 (mtp) REVERT: E 474 VAL cc_start: 0.9411 (t) cc_final: 0.9209 (p) REVERT: E 497 ILE cc_start: 0.9509 (mm) cc_final: 0.9195 (mm) REVERT: E 540 ARG cc_start: 0.8623 (mtt180) cc_final: 0.7855 (mtm-85) REVERT: E 600 MET cc_start: 0.8533 (mtt) cc_final: 0.8308 (mtt) REVERT: E 618 LYS cc_start: 0.8160 (ttmt) cc_final: 0.6811 (ttmt) REVERT: E 650 ILE cc_start: 0.9042 (tp) cc_final: 0.8502 (tp) REVERT: E 675 HIS cc_start: 0.7943 (m170) cc_final: 0.7583 (m-70) REVERT: E 678 MET cc_start: 0.8638 (mtm) cc_final: 0.8213 (mtm) REVERT: E 680 TYR cc_start: 0.8986 (t80) cc_final: 0.8762 (t80) REVERT: E 702 HIS cc_start: 0.8826 (m90) cc_final: 0.8441 (m90) REVERT: F 339 MET cc_start: 0.9430 (tpp) cc_final: 0.9214 (tpp) REVERT: F 371 GLN cc_start: 0.9054 (tt0) cc_final: 0.8422 (tm-30) REVERT: F 425 GLU cc_start: 0.8551 (tt0) cc_final: 0.8259 (tm-30) REVERT: F 441 LEU cc_start: 0.9003 (mt) cc_final: 0.8769 (mt) REVERT: F 464 VAL cc_start: 0.9121 (t) cc_final: 0.8895 (m) REVERT: F 496 MET cc_start: 0.8986 (mmm) cc_final: 0.8765 (mmm) outliers start: 2 outliers final: 0 residues processed: 480 average time/residue: 0.3180 time to fit residues: 226.5789 Evaluate side-chains 341 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 2.824 ------------------------------------------------------------------------------- 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: 6.9990 chunk 66 optimal weight: 0.9980 chunk 178 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 435 HIS C 631 GLN D 419 GLN E 477 ASN ** E 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3131 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= 0.278 Angle : 0.746 14.426 26313 Z= 0.358 Chirality : 0.047 0.197 3140 Planarity : 0.005 0.054 3226 Dihedral : 14.489 165.639 2973 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % 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: -2.26 (0.17), residues: 2343 helix: -0.44 (0.18), residues: 880 sheet: -1.25 (0.27), residues: 376 loop : -2.51 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 530 HIS 0.008 0.001 HIS B 625 PHE 0.014 0.002 PHE C 423 TYR 0.033 0.002 TYR E 432 ARG 0.004 0.000 ARG A 649 *********************** 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 434 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 433 time to evaluate : 2.181 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: A 420 MET cc_start: 0.8051 (ttp) cc_final: 0.7645 (ttp) REVERT: A 435 HIS cc_start: 0.9129 (t-90) cc_final: 0.8498 (t-90) REVERT: A 481 LEU cc_start: 0.9763 (mm) cc_final: 0.9562 (mm) REVERT: A 521 MET cc_start: 0.7710 (ptp) cc_final: 0.6584 (ptp) REVERT: A 609 GLU cc_start: 0.8326 (tp30) cc_final: 0.7909 (tp30) REVERT: A 626 LEU cc_start: 0.9687 (tp) cc_final: 0.9458 (tp) REVERT: A 650 ILE cc_start: 0.9233 (mt) cc_final: 0.8780 (mt) REVERT: A 699 ASP cc_start: 0.9150 (m-30) cc_final: 0.8843 (t70) REVERT: B 369 GLU cc_start: 0.7603 (tp30) cc_final: 0.7363 (tp30) REVERT: B 419 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 432 TYR cc_start: 0.9413 (t80) cc_final: 0.9033 (t80) REVERT: B 445 HIS cc_start: 0.8577 (m-70) cc_final: 0.7956 (m-70) REVERT: B 447 ILE cc_start: 0.8298 (mm) cc_final: 0.8024 (mm) REVERT: B 495 ILE cc_start: 0.9439 (pt) cc_final: 0.9205 (mm) REVERT: B 519 THR cc_start: 0.8310 (p) cc_final: 0.8052 (p) REVERT: B 535 MET cc_start: 0.9220 (tmm) cc_final: 0.8797 (tmm) REVERT: B 542 MET cc_start: 0.9185 (ttp) cc_final: 0.8751 (ttp) REVERT: B 556 LYS cc_start: 0.9351 (mmpt) cc_final: 0.8868 (ptmm) REVERT: B 653 GLN cc_start: 0.6963 (pp30) cc_final: 0.6652 (pp30) REVERT: B 671 GLN cc_start: 0.7036 (tp40) cc_final: 0.6723 (tp-100) REVERT: B 699 ASP cc_start: 0.8908 (m-30) cc_final: 0.8643 (t70) REVERT: C 425 GLU cc_start: 0.9317 (tt0) cc_final: 0.8678 (tm-30) REVERT: C 459 MET cc_start: 0.8860 (mtt) cc_final: 0.8628 (mtt) REVERT: C 507 TYR cc_start: 0.8803 (m-80) cc_final: 0.8253 (m-80) REVERT: C 522 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7433 (mtmt) REVERT: C 535 MET cc_start: 0.8879 (tmm) cc_final: 0.8658 (tmm) REVERT: C 666 GLN cc_start: 0.6702 (mp10) cc_final: 0.6491 (mp10) REVERT: D 318 LEU cc_start: 0.9357 (tp) cc_final: 0.9145 (mp) REVERT: D 406 LYS cc_start: 0.9087 (mttt) cc_final: 0.8781 (mtpm) REVERT: D 425 GLU cc_start: 0.8447 (tt0) cc_final: 0.7388 (tp30) REVERT: D 426 VAL cc_start: 0.9010 (t) cc_final: 0.8697 (t) REVERT: D 441 LEU cc_start: 0.8947 (mt) cc_final: 0.8604 (mt) REVERT: D 447 ILE cc_start: 0.9585 (pt) cc_final: 0.9215 (mp) REVERT: D 462 LEU cc_start: 0.9530 (pp) cc_final: 0.9317 (pp) REVERT: D 479 MET cc_start: 0.9272 (mtt) cc_final: 0.8808 (mtm) REVERT: D 595 ASP cc_start: 0.8219 (t0) cc_final: 0.7971 (t0) REVERT: D 603 ILE cc_start: 0.8367 (mm) cc_final: 0.8101 (mm) REVERT: D 607 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7936 (mmmt) REVERT: D 610 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8515 (pp20) REVERT: D 614 ARG cc_start: 0.8758 (mtt180) cc_final: 0.8451 (mmt90) REVERT: D 617 GLN cc_start: 0.9241 (tt0) cc_final: 0.8916 (tm-30) REVERT: D 632 ARG cc_start: 0.8470 (ptt180) cc_final: 0.7844 (tpm170) REVERT: E 369 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7300 (mt-10) REVERT: E 422 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8000 (mmm-85) REVERT: E 432 TYR cc_start: 0.8662 (t80) cc_final: 0.8427 (t80) REVERT: E 459 MET cc_start: 0.9229 (mtp) cc_final: 0.8482 (mtp) REVERT: E 540 ARG cc_start: 0.8389 (mtt180) cc_final: 0.7935 (mtm-85) REVERT: E 650 ILE cc_start: 0.9219 (tp) cc_final: 0.8655 (tp) REVERT: E 670 GLU cc_start: 0.8705 (pm20) cc_final: 0.8206 (pm20) REVERT: E 675 HIS cc_start: 0.7911 (m170) cc_final: 0.7699 (m90) REVERT: E 678 MET cc_start: 0.8509 (mtm) cc_final: 0.8063 (mtm) REVERT: E 702 HIS cc_start: 0.8799 (m90) cc_final: 0.8372 (m90) REVERT: F 339 MET cc_start: 0.9430 (tpp) cc_final: 0.9189 (tpp) REVERT: F 371 GLN cc_start: 0.9023 (tt0) cc_final: 0.8402 (tm-30) REVERT: F 441 LEU cc_start: 0.9015 (mt) cc_final: 0.8736 (mt) REVERT: F 479 MET cc_start: 0.9260 (mtm) cc_final: 0.8914 (mtm) REVERT: F 496 MET cc_start: 0.8980 (mmm) cc_final: 0.8669 (mpp) REVERT: F 529 ARG cc_start: 0.9055 (mpt-90) cc_final: 0.8768 (mtm-85) REVERT: F 641 LEU cc_start: 0.9500 (mt) cc_final: 0.9184 (mp) REVERT: F 659 ASP cc_start: 0.7489 (m-30) cc_final: 0.7237 (m-30) REVERT: F 680 TYR cc_start: 0.9163 (t80) cc_final: 0.8480 (t80) outliers start: 1 outliers final: 0 residues processed: 434 average time/residue: 0.3405 time to fit residues: 223.2456 Evaluate side-chains 341 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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: 10.0000 chunk 161 optimal weight: 0.0770 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 144 optimal weight: 0.0030 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 112 optimal weight: 0.2980 chunk 204 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 415 ASN C 435 HIS D 419 GLN E 415 ASN ** E 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 GLN F 675 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19276 Z= 0.203 Angle : 0.700 9.552 26313 Z= 0.333 Chirality : 0.046 0.234 3140 Planarity : 0.005 0.058 3226 Dihedral : 14.156 167.590 2973 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -1.82 (0.17), residues: 2343 helix: -0.09 (0.18), residues: 911 sheet: -1.01 (0.27), residues: 387 loop : -2.30 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 530 HIS 0.007 0.001 HIS B 625 PHE 0.019 0.001 PHE A 485 TYR 0.022 0.002 TYR E 432 ARG 0.008 0.000 ARG B 529 *********************** 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 446 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 2.082 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: A 435 HIS cc_start: 0.9181 (t-90) cc_final: 0.8546 (t-90) REVERT: A 521 MET cc_start: 0.7533 (ptp) cc_final: 0.6689 (ptp) REVERT: A 609 GLU cc_start: 0.8364 (tp30) cc_final: 0.7985 (tp30) REVERT: A 626 LEU cc_start: 0.9690 (tp) cc_final: 0.9486 (tp) REVERT: A 671 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7591 (tm-30) REVERT: A 675 HIS cc_start: 0.7582 (m170) cc_final: 0.7220 (m-70) REVERT: A 699 ASP cc_start: 0.9168 (m-30) cc_final: 0.8831 (t70) REVERT: B 419 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 432 TYR cc_start: 0.9421 (t80) cc_final: 0.9030 (t80) REVERT: B 445 HIS cc_start: 0.8447 (m-70) cc_final: 0.7879 (m-70) REVERT: B 447 ILE cc_start: 0.8225 (mm) cc_final: 0.7943 (mm) REVERT: B 496 MET cc_start: 0.7878 (pmm) cc_final: 0.7207 (ppp) REVERT: B 529 ARG cc_start: 0.8446 (mpp-170) cc_final: 0.7888 (mtm-85) REVERT: B 535 MET cc_start: 0.9148 (tmm) cc_final: 0.8811 (tmm) REVERT: B 538 ARG cc_start: 0.6957 (ptp-170) cc_final: 0.6301 (mtm180) REVERT: B 542 MET cc_start: 0.9087 (ttp) cc_final: 0.8461 (ttp) REVERT: B 556 LYS cc_start: 0.9322 (mmpt) cc_final: 0.8875 (ptmm) REVERT: B 699 ASP cc_start: 0.8872 (m-30) cc_final: 0.8627 (t70) REVERT: C 365 ILE cc_start: 0.9139 (pt) cc_final: 0.8787 (mm) REVERT: C 425 GLU cc_start: 0.9290 (tt0) cc_final: 0.8634 (tm-30) REVERT: C 507 TYR cc_start: 0.8738 (m-80) cc_final: 0.8198 (m-80) REVERT: C 522 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7313 (mtmt) REVERT: D 369 GLU cc_start: 0.7578 (tt0) cc_final: 0.6627 (tt0) REVERT: D 425 GLU cc_start: 0.8383 (tt0) cc_final: 0.7327 (tp30) REVERT: D 426 VAL cc_start: 0.8935 (t) cc_final: 0.8612 (t) REVERT: D 441 LEU cc_start: 0.8868 (mt) cc_final: 0.8566 (mt) REVERT: D 447 ILE cc_start: 0.9584 (pt) cc_final: 0.9218 (mp) REVERT: D 479 MET cc_start: 0.9284 (mtt) cc_final: 0.8773 (mtm) REVERT: D 595 ASP cc_start: 0.8203 (t0) cc_final: 0.7980 (t0) REVERT: D 607 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7923 (mmmt) REVERT: D 610 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8392 (pp20) REVERT: D 632 ARG cc_start: 0.8287 (ptt180) cc_final: 0.7758 (tpm170) REVERT: D 671 GLN cc_start: 0.9094 (mp10) cc_final: 0.8841 (mm-40) REVERT: E 369 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7108 (mt-10) REVERT: E 422 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.7926 (mmm-85) REVERT: E 456 LEU cc_start: 0.9297 (tp) cc_final: 0.9045 (tp) REVERT: E 459 MET cc_start: 0.9192 (mtp) cc_final: 0.8493 (mtp) REVERT: E 461 HIS cc_start: 0.8605 (m-70) cc_final: 0.8279 (m-70) REVERT: E 540 ARG cc_start: 0.8459 (mtt180) cc_final: 0.7889 (mtm-85) REVERT: E 555 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8019 (tmm-80) REVERT: E 650 ILE cc_start: 0.9182 (tp) cc_final: 0.8753 (tp) REVERT: E 670 GLU cc_start: 0.8544 (pm20) cc_final: 0.8171 (pm20) REVERT: E 702 HIS cc_start: 0.8791 (m90) cc_final: 0.8257 (m90) REVERT: F 339 MET cc_start: 0.9405 (tpp) cc_final: 0.9140 (tpp) REVERT: F 344 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8243 (mt-10) REVERT: F 371 GLN cc_start: 0.8953 (tt0) cc_final: 0.8260 (tm-30) REVERT: F 425 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7821 (tm-30) REVERT: F 441 LEU cc_start: 0.8984 (mt) cc_final: 0.8667 (mt) REVERT: F 479 MET cc_start: 0.9282 (mtm) cc_final: 0.8966 (mtm) REVERT: F 496 MET cc_start: 0.9004 (mmm) cc_final: 0.8662 (mmm) REVERT: F 510 ILE cc_start: 0.9277 (pt) cc_final: 0.8931 (mt) REVERT: F 529 ARG cc_start: 0.8989 (mpt-90) cc_final: 0.8754 (mtm-85) REVERT: F 641 LEU cc_start: 0.9342 (mt) cc_final: 0.9069 (mp) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.3153 time to fit residues: 209.8362 Evaluate side-chains 343 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 204 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN D 419 GLN ** E 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19276 Z= 0.306 Angle : 0.756 10.926 26313 Z= 0.360 Chirality : 0.047 0.246 3140 Planarity : 0.005 0.051 3226 Dihedral : 14.005 151.724 2973 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % 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: -1.60 (0.17), residues: 2343 helix: 0.08 (0.18), residues: 897 sheet: -0.87 (0.27), residues: 370 loop : -2.15 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 530 HIS 0.008 0.001 HIS B 625 PHE 0.016 0.002 PHE A 553 TYR 0.019 0.002 TYR E 432 ARG 0.014 0.001 ARG B 529 *********************** 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 419 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 418 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.8205 (ptp) cc_final: 0.7875 (ptp) REVERT: A 542 MET cc_start: 0.7868 (mmm) cc_final: 0.7635 (mmt) REVERT: A 609 GLU cc_start: 0.8500 (tp30) cc_final: 0.8219 (tp30) REVERT: A 618 LYS cc_start: 0.8009 (ptpt) cc_final: 0.7782 (ptmt) REVERT: A 671 GLN cc_start: 0.7767 (tm-30) cc_final: 0.7507 (tm-30) REVERT: A 699 ASP cc_start: 0.9167 (m-30) cc_final: 0.8855 (t70) REVERT: B 419 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7962 (tm-30) REVERT: B 432 TYR cc_start: 0.9476 (t80) cc_final: 0.9016 (t80) REVERT: B 529 ARG cc_start: 0.8473 (mpp-170) cc_final: 0.8003 (mtm-85) REVERT: B 535 MET cc_start: 0.9234 (tmm) cc_final: 0.8967 (tmm) REVERT: B 542 MET cc_start: 0.9119 (ttp) cc_final: 0.8720 (ttp) REVERT: B 545 MET cc_start: 0.7883 (mpp) cc_final: 0.7527 (mpp) REVERT: B 556 LYS cc_start: 0.9292 (mmpt) cc_final: 0.8950 (pttp) REVERT: B 610 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8502 (pp20) REVERT: B 671 GLN cc_start: 0.6866 (tp40) cc_final: 0.6615 (tp-100) REVERT: B 699 ASP cc_start: 0.8916 (m-30) cc_final: 0.8662 (t70) REVERT: C 425 GLU cc_start: 0.9316 (tt0) cc_final: 0.8586 (tm-30) REVERT: C 507 TYR cc_start: 0.8876 (m-80) cc_final: 0.8310 (m-80) REVERT: C 522 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7415 (mtmt) REVERT: D 425 GLU cc_start: 0.8515 (tt0) cc_final: 0.7443 (tp30) REVERT: D 441 LEU cc_start: 0.9019 (mt) cc_final: 0.8622 (mt) REVERT: D 479 MET cc_start: 0.9294 (mtt) cc_final: 0.8687 (mtm) REVERT: D 482 SER cc_start: 0.9572 (m) cc_final: 0.9370 (p) REVERT: D 602 MET cc_start: 0.8649 (tmm) cc_final: 0.8340 (tpp) REVERT: D 607 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7691 (pttm) REVERT: D 631 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7993 (mm-40) REVERT: D 632 ARG cc_start: 0.8664 (ptt180) cc_final: 0.7976 (tpm170) REVERT: E 369 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7234 (mt-10) REVERT: E 422 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: E 459 MET cc_start: 0.9260 (mtp) cc_final: 0.8554 (mtp) REVERT: E 461 HIS cc_start: 0.8778 (m-70) cc_final: 0.8473 (m-70) REVERT: E 540 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7887 (mtm-85) REVERT: E 555 ARG cc_start: 0.8750 (tmm-80) cc_final: 0.8198 (tmm-80) REVERT: E 650 ILE cc_start: 0.8962 (tp) cc_final: 0.8441 (tp) REVERT: E 670 GLU cc_start: 0.8626 (pm20) cc_final: 0.8409 (pm20) REVERT: E 678 MET cc_start: 0.8258 (mtm) cc_final: 0.8032 (mtm) REVERT: E 680 TYR cc_start: 0.9127 (t80) cc_final: 0.8907 (t80) REVERT: F 339 MET cc_start: 0.9409 (tpp) cc_final: 0.9133 (tpp) REVERT: F 371 GLN cc_start: 0.8988 (tt0) cc_final: 0.8341 (tm-30) REVERT: F 441 LEU cc_start: 0.8873 (mt) cc_final: 0.8612 (mt) REVERT: F 479 MET cc_start: 0.9178 (mtm) cc_final: 0.8913 (mtm) REVERT: F 496 MET cc_start: 0.9031 (mmt) cc_final: 0.8778 (mmm) REVERT: F 529 ARG cc_start: 0.9134 (mpt-90) cc_final: 0.8704 (mtm-85) REVERT: F 641 LEU cc_start: 0.9392 (mt) cc_final: 0.9191 (mp) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.3068 time to fit residues: 194.3242 Evaluate side-chains 322 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 321 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN D 419 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 675 HIS F 666 GLN F 675 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3970 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= 0.325 Angle : 0.770 11.040 26313 Z= 0.368 Chirality : 0.048 0.216 3140 Planarity : 0.005 0.054 3226 Dihedral : 13.876 147.602 2973 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % 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: -1.50 (0.18), residues: 2343 helix: 0.07 (0.18), residues: 898 sheet: -0.76 (0.28), residues: 369 loop : -2.02 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 530 HIS 0.006 0.001 HIS B 625 PHE 0.017 0.002 PHE D 553 TYR 0.029 0.002 TYR E 432 ARG 0.013 0.000 ARG B 529 *********************** 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 412 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 411 time to evaluate : 1.934 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: A 542 MET cc_start: 0.7803 (mmm) cc_final: 0.7582 (mmt) REVERT: A 609 GLU cc_start: 0.8541 (tp30) cc_final: 0.8268 (tp30) REVERT: A 671 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 699 ASP cc_start: 0.9131 (m-30) cc_final: 0.8817 (t70) REVERT: B 419 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 432 TYR cc_start: 0.9459 (t80) cc_final: 0.9039 (t80) REVERT: B 535 MET cc_start: 0.9187 (tmm) cc_final: 0.8953 (tmm) REVERT: B 538 ARG cc_start: 0.7029 (ptp-170) cc_final: 0.6409 (mtm180) REVERT: B 542 MET cc_start: 0.9058 (ttp) cc_final: 0.8371 (ttp) REVERT: B 556 LYS cc_start: 0.9250 (mmpt) cc_final: 0.8954 (pttp) REVERT: B 699 ASP cc_start: 0.8932 (m-30) cc_final: 0.8683 (t70) REVERT: C 425 GLU cc_start: 0.9327 (tt0) cc_final: 0.8561 (tm-30) REVERT: C 462 LEU cc_start: 0.9068 (tt) cc_final: 0.8551 (tp) REVERT: C 507 TYR cc_start: 0.8802 (m-80) cc_final: 0.8362 (m-80) REVERT: C 673 LEU cc_start: 0.8697 (mt) cc_final: 0.8465 (mt) REVERT: D 369 GLU cc_start: 0.7403 (tt0) cc_final: 0.7023 (tt0) REVERT: D 425 GLU cc_start: 0.8495 (tt0) cc_final: 0.7450 (tp30) REVERT: D 426 VAL cc_start: 0.9040 (t) cc_final: 0.8664 (t) REVERT: D 441 LEU cc_start: 0.9066 (mt) cc_final: 0.8672 (mt) REVERT: D 479 MET cc_start: 0.9293 (mtt) cc_final: 0.8649 (mtm) REVERT: D 501 MET cc_start: 0.8051 (tmm) cc_final: 0.7770 (tmm) REVERT: D 602 MET cc_start: 0.8345 (tmm) cc_final: 0.7763 (tmm) REVERT: D 631 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7861 (mm-40) REVERT: D 632 ARG cc_start: 0.8683 (ptt180) cc_final: 0.7967 (tpm170) REVERT: E 422 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.8140 (mmm-85) REVERT: E 459 MET cc_start: 0.9281 (mtp) cc_final: 0.8499 (mtp) REVERT: E 461 HIS cc_start: 0.8738 (m-70) cc_final: 0.8532 (m-70) REVERT: E 540 ARG cc_start: 0.8417 (mtt180) cc_final: 0.7857 (mtm-85) REVERT: E 555 ARG cc_start: 0.8770 (tmm-80) cc_final: 0.8254 (tmm-80) REVERT: E 650 ILE cc_start: 0.8947 (tp) cc_final: 0.8416 (tp) REVERT: E 675 HIS cc_start: 0.8298 (m-70) cc_final: 0.7735 (m90) REVERT: E 678 MET cc_start: 0.8346 (mtm) cc_final: 0.8074 (mtm) REVERT: E 680 TYR cc_start: 0.9091 (t80) cc_final: 0.8840 (t80) REVERT: F 334 GLU cc_start: 0.8925 (tp30) cc_final: 0.8682 (tp30) REVERT: F 339 MET cc_start: 0.9430 (tpp) cc_final: 0.9160 (tpp) REVERT: F 371 GLN cc_start: 0.8982 (tt0) cc_final: 0.8269 (tm-30) REVERT: F 441 LEU cc_start: 0.8875 (mt) cc_final: 0.8591 (mt) REVERT: F 479 MET cc_start: 0.9200 (mtm) cc_final: 0.8842 (mtm) REVERT: F 496 MET cc_start: 0.9074 (mmt) cc_final: 0.8810 (mmm) REVERT: F 529 ARG cc_start: 0.9238 (mpt-90) cc_final: 0.8638 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.3045 time to fit residues: 190.8802 Evaluate side-chains 317 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 2.395 ------------------------------------------------------------------------------- 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: 0.5980 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 166 optimal weight: 0.0770 chunk 129 optimal weight: 0.4980 chunk 192 optimal weight: 6.9990 chunk 127 optimal weight: 0.2980 chunk 227 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN B 671 GLN C 435 HIS ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 HIS ** E 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8279 moved from start: 0.4368 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= 0.175 Angle : 0.704 10.355 26313 Z= 0.331 Chirality : 0.046 0.194 3140 Planarity : 0.005 0.066 3226 Dihedral : 13.514 145.650 2973 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -1.04 (0.18), residues: 2343 helix: 0.58 (0.19), residues: 872 sheet: -0.52 (0.28), residues: 367 loop : -1.83 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 530 HIS 0.006 0.001 HIS A 625 PHE 0.019 0.002 PHE F 597 TYR 0.020 0.002 TYR E 432 ARG 0.005 0.000 ARG B 529 *********************** 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 443 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 3.347 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: A 481 LEU cc_start: 0.9705 (mm) cc_final: 0.9493 (mm) REVERT: A 508 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7634 (tp30) REVERT: A 517 VAL cc_start: 0.9130 (m) cc_final: 0.8785 (t) REVERT: A 521 MET cc_start: 0.8342 (ptp) cc_final: 0.7781 (ptp) REVERT: A 542 MET cc_start: 0.7789 (mmm) cc_final: 0.7551 (mmt) REVERT: A 609 GLU cc_start: 0.8436 (tp30) cc_final: 0.8157 (tp30) REVERT: A 671 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 699 ASP cc_start: 0.9133 (m-30) cc_final: 0.8822 (t70) REVERT: B 419 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 432 TYR cc_start: 0.9370 (t80) cc_final: 0.8983 (t80) REVERT: B 445 HIS cc_start: 0.8490 (m-70) cc_final: 0.7975 (m-70) REVERT: B 477 ASN cc_start: 0.8790 (m-40) cc_final: 0.8581 (m-40) REVERT: B 496 MET cc_start: 0.7947 (pmm) cc_final: 0.7194 (ppp) REVERT: B 529 ARG cc_start: 0.8464 (mpp-170) cc_final: 0.7663 (mpp80) REVERT: B 538 ARG cc_start: 0.6883 (ptp-170) cc_final: 0.6286 (mtm180) REVERT: B 542 MET cc_start: 0.8993 (ttp) cc_final: 0.8529 (ttp) REVERT: B 556 LYS cc_start: 0.9258 (mmpt) cc_final: 0.8968 (pttp) REVERT: B 699 ASP cc_start: 0.8886 (m-30) cc_final: 0.8608 (t70) REVERT: C 425 GLU cc_start: 0.9284 (tt0) cc_final: 0.8528 (tm-30) REVERT: C 462 LEU cc_start: 0.9002 (tt) cc_final: 0.8795 (tp) REVERT: C 507 TYR cc_start: 0.8721 (m-80) cc_final: 0.8222 (m-80) REVERT: C 590 ILE cc_start: 0.9582 (mt) cc_final: 0.9181 (tt) REVERT: D 441 LEU cc_start: 0.8763 (mt) cc_final: 0.8414 (mt) REVERT: D 447 ILE cc_start: 0.9621 (pt) cc_final: 0.9219 (mt) REVERT: D 479 MET cc_start: 0.9184 (mtt) cc_final: 0.8635 (mtm) REVERT: D 501 MET cc_start: 0.7927 (tmm) cc_final: 0.7637 (tmm) REVERT: D 602 MET cc_start: 0.8557 (tmm) cc_final: 0.8207 (tmm) REVERT: D 617 GLN cc_start: 0.9143 (tt0) cc_final: 0.8870 (tm-30) REVERT: D 631 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7857 (mm-40) REVERT: E 369 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7123 (mt-10) REVERT: E 422 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8148 (mmm-85) REVERT: E 455 ASP cc_start: 0.8768 (t0) cc_final: 0.8541 (t70) REVERT: E 459 MET cc_start: 0.9096 (mtp) cc_final: 0.8558 (mtp) REVERT: E 461 HIS cc_start: 0.8387 (m-70) cc_final: 0.8126 (m-70) REVERT: E 521 MET cc_start: 0.7221 (tmm) cc_final: 0.6551 (tmm) REVERT: E 540 ARG cc_start: 0.8398 (mtt180) cc_final: 0.7881 (mtm-85) REVERT: E 555 ARG cc_start: 0.8758 (tmm-80) cc_final: 0.8350 (tmm-80) REVERT: E 650 ILE cc_start: 0.9042 (tp) cc_final: 0.8497 (tp) REVERT: E 675 HIS cc_start: 0.8209 (m-70) cc_final: 0.7752 (m90) REVERT: E 678 MET cc_start: 0.8072 (mtm) cc_final: 0.7791 (mtm) REVERT: E 680 TYR cc_start: 0.9037 (t80) cc_final: 0.8822 (t80) REVERT: F 339 MET cc_start: 0.9416 (tpp) cc_final: 0.9122 (tpp) REVERT: F 371 GLN cc_start: 0.8908 (tt0) cc_final: 0.8186 (tm-30) REVERT: F 419 GLN cc_start: 0.9066 (tt0) cc_final: 0.8695 (tm-30) REVERT: F 420 MET cc_start: 0.7864 (mmt) cc_final: 0.7663 (mmt) REVERT: F 425 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8030 (tm-30) REVERT: F 441 LEU cc_start: 0.8925 (mt) cc_final: 0.8684 (mt) REVERT: F 479 MET cc_start: 0.9132 (mtm) cc_final: 0.8842 (mtm) REVERT: F 496 MET cc_start: 0.9192 (mmt) cc_final: 0.8731 (mmm) REVERT: F 510 ILE cc_start: 0.9177 (pt) cc_final: 0.8922 (mt) REVERT: F 626 LEU cc_start: 0.9347 (tp) cc_final: 0.9140 (tp) REVERT: F 641 LEU cc_start: 0.8990 (mp) cc_final: 0.8266 (mp) REVERT: F 680 TYR cc_start: 0.9094 (t80) cc_final: 0.8605 (t80) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.3109 time to fit residues: 212.6539 Evaluate side-chains 331 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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: 0.8980 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 206 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN C 435 HIS ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 HIS E 617 GLN F 617 GLN F 666 GLN F 675 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19276 Z= 0.213 Angle : 0.708 10.806 26313 Z= 0.332 Chirality : 0.046 0.233 3140 Planarity : 0.005 0.053 3226 Dihedral : 13.361 139.845 2973 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -0.94 (0.18), residues: 2343 helix: 0.62 (0.19), residues: 873 sheet: -0.42 (0.28), residues: 351 loop : -1.73 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 530 HIS 0.005 0.001 HIS B 625 PHE 0.013 0.002 PHE E 652 TYR 0.018 0.001 TYR B 680 ARG 0.014 0.000 ARG F 529 *********************** 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 418 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 2.107 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: A 508 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7633 (tp30) REVERT: A 517 VAL cc_start: 0.9195 (m) cc_final: 0.8781 (t) REVERT: A 521 MET cc_start: 0.8286 (ptp) cc_final: 0.7818 (ptp) REVERT: A 595 ASP cc_start: 0.7585 (t70) cc_final: 0.6934 (t70) REVERT: A 596 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 609 GLU cc_start: 0.8454 (tp30) cc_final: 0.8160 (tp30) REVERT: A 671 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7444 (tm-30) REVERT: A 699 ASP cc_start: 0.9176 (m-30) cc_final: 0.8878 (t70) REVERT: B 419 GLN cc_start: 0.8529 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 432 TYR cc_start: 0.9415 (t80) cc_final: 0.9022 (t80) REVERT: B 477 ASN cc_start: 0.8796 (m-40) cc_final: 0.8558 (m110) REVERT: B 535 MET cc_start: 0.9166 (tmm) cc_final: 0.8945 (tmm) REVERT: B 538 ARG cc_start: 0.7094 (ptp-170) cc_final: 0.6483 (mtm180) REVERT: B 542 MET cc_start: 0.8986 (ttp) cc_final: 0.8537 (ttp) REVERT: B 556 LYS cc_start: 0.9250 (mmpt) cc_final: 0.8970 (pttp) REVERT: B 699 ASP cc_start: 0.8899 (m-30) cc_final: 0.8626 (t70) REVERT: C 425 GLU cc_start: 0.9302 (tt0) cc_final: 0.8641 (tm-30) REVERT: C 507 TYR cc_start: 0.8734 (m-80) cc_final: 0.8300 (m-80) REVERT: C 541 LEU cc_start: 0.9031 (tt) cc_final: 0.8646 (pp) REVERT: C 590 ILE cc_start: 0.9565 (mt) cc_final: 0.9140 (tt) REVERT: D 447 ILE cc_start: 0.9607 (pt) cc_final: 0.9205 (mt) REVERT: D 479 MET cc_start: 0.9112 (mtt) cc_final: 0.8909 (mtm) REVERT: D 501 MET cc_start: 0.7990 (tmm) cc_final: 0.7662 (tmm) REVERT: D 602 MET cc_start: 0.8108 (tmm) cc_final: 0.7746 (tmm) REVERT: D 631 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7864 (mm-40) REVERT: D 632 ARG cc_start: 0.8385 (ptt180) cc_final: 0.7692 (tpm170) REVERT: E 369 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7401 (mt-10) REVERT: E 422 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.8156 (mmm-85) REVERT: E 456 LEU cc_start: 0.9308 (tp) cc_final: 0.8932 (tp) REVERT: E 459 MET cc_start: 0.9222 (mtp) cc_final: 0.8293 (mtp) REVERT: E 461 HIS cc_start: 0.8424 (m-70) cc_final: 0.8150 (m-70) REVERT: E 521 MET cc_start: 0.7238 (tmm) cc_final: 0.6809 (tmm) REVERT: E 540 ARG cc_start: 0.8439 (mtt180) cc_final: 0.7953 (mtm-85) REVERT: E 618 LYS cc_start: 0.8122 (mttm) cc_final: 0.7724 (mttm) REVERT: E 650 ILE cc_start: 0.8996 (tp) cc_final: 0.8668 (tp) REVERT: E 675 HIS cc_start: 0.8245 (m-70) cc_final: 0.7682 (m90) REVERT: E 680 TYR cc_start: 0.9192 (t80) cc_final: 0.8961 (t80) REVERT: F 339 MET cc_start: 0.9401 (tpp) cc_final: 0.9102 (tpp) REVERT: F 371 GLN cc_start: 0.8908 (tt0) cc_final: 0.8194 (tm-30) REVERT: F 419 GLN cc_start: 0.9059 (tt0) cc_final: 0.8687 (tm-30) REVERT: F 420 MET cc_start: 0.7845 (mmt) cc_final: 0.7640 (mmt) REVERT: F 441 LEU cc_start: 0.8794 (mt) cc_final: 0.8514 (mt) REVERT: F 479 MET cc_start: 0.9156 (mtm) cc_final: 0.8818 (mtm) REVERT: F 496 MET cc_start: 0.9227 (mmt) cc_final: 0.8749 (mmm) REVERT: F 500 LYS cc_start: 0.7754 (pttt) cc_final: 0.7324 (pttt) REVERT: F 510 ILE cc_start: 0.9181 (pt) cc_final: 0.8881 (mt) REVERT: F 641 LEU cc_start: 0.9007 (mp) cc_final: 0.8090 (mp) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.3075 time to fit residues: 196.9203 Evaluate side-chains 326 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 2.186 ------------------------------------------------------------------------------- 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: 1.9990 chunk 198 optimal weight: 6.9990 chunk 211 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN C 435 HIS D 419 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 ASN F 617 GLN F 675 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19276 Z= 0.195 Angle : 0.702 10.728 26313 Z= 0.328 Chirality : 0.046 0.253 3140 Planarity : 0.005 0.054 3226 Dihedral : 13.289 138.836 2973 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.05 % Allowed : 0.80 % Favored : 99.15 % 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: -0.77 (0.18), residues: 2343 helix: 0.66 (0.19), residues: 880 sheet: -0.16 (0.27), residues: 373 loop : -1.63 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 530 HIS 0.004 0.001 HIS C 512 PHE 0.026 0.002 PHE F 597 TYR 0.019 0.001 TYR B 680 ARG 0.011 0.000 ARG F 529 *********************** 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 415 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 2.128 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: A 435 HIS cc_start: 0.9282 (t-90) cc_final: 0.8730 (t-90) REVERT: A 508 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7615 (tp30) REVERT: A 517 VAL cc_start: 0.9148 (m) cc_final: 0.8810 (t) REVERT: A 521 MET cc_start: 0.8258 (ptp) cc_final: 0.7559 (ptp) REVERT: A 596 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8239 (mm-30) REVERT: A 609 GLU cc_start: 0.8409 (tp30) cc_final: 0.8170 (tp30) REVERT: A 699 ASP cc_start: 0.9153 (m-30) cc_final: 0.8871 (t70) REVERT: B 419 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 432 TYR cc_start: 0.9398 (t80) cc_final: 0.8974 (t80) REVERT: B 459 MET cc_start: 0.8701 (ptt) cc_final: 0.8371 (ptp) REVERT: B 535 MET cc_start: 0.9147 (tmm) cc_final: 0.8891 (tmm) REVERT: B 542 MET cc_start: 0.8951 (ttp) cc_final: 0.8551 (ttp) REVERT: B 556 LYS cc_start: 0.9250 (mmpt) cc_final: 0.8944 (ptmm) REVERT: B 699 ASP cc_start: 0.8859 (m-30) cc_final: 0.8582 (t70) REVERT: C 425 GLU cc_start: 0.9286 (tt0) cc_final: 0.8619 (tm-30) REVERT: C 507 TYR cc_start: 0.8746 (m-80) cc_final: 0.8270 (m-80) REVERT: C 541 LEU cc_start: 0.9107 (tt) cc_final: 0.8708 (pp) REVERT: C 590 ILE cc_start: 0.9578 (mt) cc_final: 0.9140 (tt) REVERT: D 369 GLU cc_start: 0.7504 (tt0) cc_final: 0.6993 (tt0) REVERT: D 425 GLU cc_start: 0.8268 (tt0) cc_final: 0.7271 (tp30) REVERT: D 447 ILE cc_start: 0.9591 (pt) cc_final: 0.9212 (mp) REVERT: D 479 MET cc_start: 0.9125 (mtt) cc_final: 0.8686 (mtt) REVERT: D 501 MET cc_start: 0.7877 (tmm) cc_final: 0.7655 (tmm) REVERT: D 595 ASP cc_start: 0.8220 (t0) cc_final: 0.8016 (t0) REVERT: D 602 MET cc_start: 0.7928 (tmm) cc_final: 0.7579 (tmm) REVERT: D 631 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7797 (mm-40) REVERT: D 632 ARG cc_start: 0.8320 (ptt180) cc_final: 0.7605 (tpm170) REVERT: E 369 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7573 (mt-10) REVERT: E 422 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8176 (mmm-85) REVERT: E 452 ILE cc_start: 0.8910 (tp) cc_final: 0.8698 (mm) REVERT: E 459 MET cc_start: 0.9163 (mtp) cc_final: 0.8482 (mtp) REVERT: E 496 MET cc_start: 0.8961 (mmm) cc_final: 0.8759 (mmm) REVERT: E 521 MET cc_start: 0.7319 (tmm) cc_final: 0.6966 (tmm) REVERT: E 537 ARG cc_start: 0.8067 (ttt90) cc_final: 0.7815 (ptm-80) REVERT: E 540 ARG cc_start: 0.8468 (mtt180) cc_final: 0.8002 (mtm-85) REVERT: E 650 ILE cc_start: 0.8866 (tp) cc_final: 0.8492 (tp) REVERT: E 675 HIS cc_start: 0.8153 (m-70) cc_final: 0.7610 (m90) REVERT: E 680 TYR cc_start: 0.9149 (t80) cc_final: 0.8939 (t80) REVERT: F 339 MET cc_start: 0.9418 (tpp) cc_final: 0.9106 (tpp) REVERT: F 371 GLN cc_start: 0.8868 (tt0) cc_final: 0.8154 (tm-30) REVERT: F 419 GLN cc_start: 0.9028 (tt0) cc_final: 0.8669 (tm-30) REVERT: F 420 MET cc_start: 0.7901 (mmt) cc_final: 0.7660 (mmt) REVERT: F 441 LEU cc_start: 0.8839 (mt) cc_final: 0.8551 (mt) REVERT: F 479 MET cc_start: 0.9106 (mtm) cc_final: 0.8836 (mtm) REVERT: F 496 MET cc_start: 0.9206 (mmt) cc_final: 0.8793 (mmm) REVERT: F 510 ILE cc_start: 0.9172 (pt) cc_final: 0.8884 (mt) REVERT: F 555 ARG cc_start: 0.8939 (mmp80) cc_final: 0.8530 (mmp80) REVERT: F 641 LEU cc_start: 0.8903 (mp) cc_final: 0.8178 (mp) outliers start: 1 outliers final: 0 residues processed: 415 average time/residue: 0.2973 time to fit residues: 187.8979 Evaluate side-chains 316 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.270 ------------------------------------------------------------------------------- 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: 7.9990 chunk 106 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 GLN C 675 HIS ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN F 617 GLN F 645 ASN F 675 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19276 Z= 0.317 Angle : 0.773 14.085 26313 Z= 0.366 Chirality : 0.048 0.264 3140 Planarity : 0.005 0.053 3226 Dihedral : 13.306 136.851 2973 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.48 (0.18), residues: 880 sheet: -0.41 (0.27), residues: 378 loop : -1.60 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 530 HIS 0.005 0.001 HIS C 461 PHE 0.020 0.002 PHE C 652 TYR 0.020 0.002 TYR A 539 ARG 0.010 0.001 ARG F 529 ********************** 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 386 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 2.082 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: A 517 VAL cc_start: 0.9216 (m) cc_final: 0.8788 (t) REVERT: A 596 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7949 (mm-30) REVERT: A 609 GLU cc_start: 0.8528 (tp30) cc_final: 0.8280 (tp30) REVERT: A 699 ASP cc_start: 0.9119 (m-30) cc_final: 0.8896 (t70) REVERT: B 419 GLN cc_start: 0.8560 (tm-30) cc_final: 0.7807 (tm-30) REVERT: B 432 TYR cc_start: 0.9463 (t80) cc_final: 0.9061 (t80) REVERT: B 479 MET cc_start: 0.9597 (mtm) cc_final: 0.9308 (mtm) REVERT: B 535 MET cc_start: 0.9171 (tmm) cc_final: 0.8911 (tmm) REVERT: B 542 MET cc_start: 0.8966 (ttp) cc_final: 0.8485 (ttp) REVERT: B 556 LYS cc_start: 0.9250 (mmpt) cc_final: 0.8929 (ptmm) REVERT: B 699 ASP cc_start: 0.8911 (m-30) cc_final: 0.8679 (t70) REVERT: C 425 GLU cc_start: 0.9307 (tt0) cc_final: 0.8540 (tm-30) REVERT: C 500 LYS cc_start: 0.8690 (pptt) cc_final: 0.8372 (mtmt) REVERT: C 507 TYR cc_start: 0.8786 (m-80) cc_final: 0.8343 (m-80) REVERT: C 590 ILE cc_start: 0.9584 (mt) cc_final: 0.9138 (tt) REVERT: D 369 GLU cc_start: 0.7403 (tt0) cc_final: 0.6907 (tt0) REVERT: D 425 GLU cc_start: 0.8420 (tt0) cc_final: 0.7423 (tp30) REVERT: D 447 ILE cc_start: 0.9618 (pt) cc_final: 0.9194 (mp) REVERT: D 501 MET cc_start: 0.7903 (tmm) cc_final: 0.7657 (tmm) REVERT: D 602 MET cc_start: 0.8067 (tmm) cc_final: 0.7641 (tmm) REVERT: D 632 ARG cc_start: 0.8504 (ptt180) cc_final: 0.7822 (tpm170) REVERT: D 678 MET cc_start: 0.8678 (ttp) cc_final: 0.8466 (ttp) REVERT: E 369 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7624 (mt-10) REVERT: E 422 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8214 (mmm-85) REVERT: E 459 MET cc_start: 0.9157 (mtp) cc_final: 0.8611 (mtp) REVERT: E 461 HIS cc_start: 0.8689 (m-70) cc_final: 0.8208 (m-70) REVERT: E 540 ARG cc_start: 0.8491 (mtt180) cc_final: 0.7991 (mtm-85) REVERT: E 593 VAL cc_start: 0.9606 (t) cc_final: 0.9339 (t) REVERT: E 617 GLN cc_start: 0.8477 (tp40) cc_final: 0.7785 (tp40) REVERT: E 618 LYS cc_start: 0.8233 (mttp) cc_final: 0.7723 (mmtp) REVERT: E 628 LEU cc_start: 0.9362 (mt) cc_final: 0.9105 (mt) REVERT: E 675 HIS cc_start: 0.8260 (m-70) cc_final: 0.7781 (m-70) REVERT: F 339 MET cc_start: 0.9425 (tpp) cc_final: 0.9125 (tpp) REVERT: F 371 GLN cc_start: 0.8931 (tt0) cc_final: 0.8220 (tm-30) REVERT: F 419 GLN cc_start: 0.9075 (tt0) cc_final: 0.8560 (tm-30) REVERT: F 441 LEU cc_start: 0.8806 (mt) cc_final: 0.8558 (mt) REVERT: F 479 MET cc_start: 0.9179 (mtm) cc_final: 0.8810 (mtm) REVERT: F 496 MET cc_start: 0.9217 (mmt) cc_final: 0.8805 (mmm) REVERT: F 641 LEU cc_start: 0.8945 (mp) cc_final: 0.8185 (mp) REVERT: F 680 TYR cc_start: 0.9322 (t80) cc_final: 0.8466 (t80) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.3052 time to fit residues: 182.8805 Evaluate side-chains 312 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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: 2.9990 chunk 172 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 187 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN C 435 HIS ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN E 526 ASN F 617 GLN ** F 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.089783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.072677 restraints weight = 56871.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.074425 restraints weight = 37162.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.075639 restraints weight = 27097.873| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19276 Z= 0.268 Angle : 0.755 12.786 26313 Z= 0.355 Chirality : 0.047 0.268 3140 Planarity : 0.005 0.057 3226 Dihedral : 13.230 138.309 2973 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.05 % Allowed : 0.40 % Favored : 99.55 % 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: -0.88 (0.18), residues: 2343 helix: 0.49 (0.18), residues: 880 sheet: -0.34 (0.27), residues: 375 loop : -1.57 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 530 HIS 0.007 0.001 HIS B 625 PHE 0.033 0.002 PHE F 597 TYR 0.019 0.002 TYR B 680 ARG 0.011 0.000 ARG F 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4255.07 seconds wall clock time: 77 minutes 50.42 seconds (4670.42 seconds total)