Starting phenix.real_space_refine on Mon Feb 19 02:33:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e89_31012/02_2024/7e89_31012.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e89_31012/02_2024/7e89_31012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e89_31012/02_2024/7e89_31012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e89_31012/02_2024/7e89_31012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e89_31012/02_2024/7e89_31012.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e89_31012/02_2024/7e89_31012.pdb" } resolution = 4.0 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= 0.002 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14972 2.51 5 N 3988 2.21 5 O 4472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 469": "OD1" <-> "OD2" Residue "I ASP 567": "OD1" <-> "OD2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 783": "OE1" <-> "OE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "B ASP 567": "OD1" <-> "OD2" 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: 23528 Number of models: 1 Model: "" Number of chains: 4 Chain: "J" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Chain: "I" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Chain: "A" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Chain: "B" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Time building chain proxies: 11.61, per 1000 atoms: 0.49 Number of scatterers: 23528 At special positions: 0 Unit cell: (171, 161, 108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4472 8.00 N 3988 7.00 C 14972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS J 349 " - pdb=" SG CYS J 356 " distance=2.03 Simple disulfide: pdb=" SG CYS J 465 " - pdb=" SG CYS J 468 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 492 " distance=2.03 Simple disulfide: pdb=" SG CYS J 673 " - pdb=" SG CYS J 784 " distance=2.03 Simple disulfide: pdb=" SG CYS I 349 " - pdb=" SG CYS I 356 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 468 " distance=2.03 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 492 " distance=2.03 Simple disulfide: pdb=" SG CYS I 673 " - pdb=" SG CYS I 784 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 784 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 465 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 673 " - pdb=" SG CYS B 784 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.65 Conformation dependent library (CDL) restraints added in 3.9 seconds 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5488 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 54 sheets defined 17.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'J' and resid 70 through 76 removed outlier: 3.788A pdb=" N LEU J 74 " --> pdb=" O THR J 70 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE J 75 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 80 Processing helix chain 'J' and resid 118 through 122 removed outlier: 4.321A pdb=" N LYS J 121 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE J 122 " --> pdb=" O GLY J 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 118 through 122' Processing helix chain 'J' and resid 229 through 234 Processing helix chain 'J' and resid 517 through 527 Processing helix chain 'J' and resid 582 through 592 Processing helix chain 'J' and resid 607 through 613 Processing helix chain 'J' and resid 619 through 634 Processing helix chain 'J' and resid 650 through 659 removed outlier: 3.980A pdb=" N TYR J 654 " --> pdb=" O ASP J 650 " (cutoff:3.500A) Processing helix chain 'J' and resid 682 through 686 Processing helix chain 'J' and resid 687 through 696 removed outlier: 4.253A pdb=" N ARG J 693 " --> pdb=" O ALA J 689 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR J 694 " --> pdb=" O PHE J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 734 through 749 removed outlier: 4.263A pdb=" N THR J 738 " --> pdb=" O HIS J 734 " (cutoff:3.500A) Processing helix chain 'J' and resid 766 through 786 removed outlier: 3.705A pdb=" N GLU J 783 " --> pdb=" O ASN J 779 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS J 784 " --> pdb=" O PHE J 780 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG J 786 " --> pdb=" O VAL J 782 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 76 removed outlier: 3.607A pdb=" N LEU I 74 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 517 through 527 Processing helix chain 'I' and resid 582 through 591 Processing helix chain 'I' and resid 607 through 613 Processing helix chain 'I' and resid 619 through 635 Processing helix chain 'I' and resid 650 through 659 removed outlier: 3.643A pdb=" N TYR I 654 " --> pdb=" O ASP I 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 696 removed outlier: 3.921A pdb=" N ARG I 693 " --> pdb=" O ALA I 689 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR I 694 " --> pdb=" O PHE I 690 " (cutoff:3.500A) Processing helix chain 'I' and resid 710 through 715 removed outlier: 3.545A pdb=" N SER I 715 " --> pdb=" O ALA I 711 " (cutoff:3.500A) Processing helix chain 'I' and resid 734 through 749 removed outlier: 4.297A pdb=" N THR I 738 " --> pdb=" O HIS I 734 " (cutoff:3.500A) Processing helix chain 'I' and resid 766 through 785 removed outlier: 4.681A pdb=" N GLU I 783 " --> pdb=" O ASN I 779 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS I 784 " --> pdb=" O PHE I 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.788A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 118 through 122 removed outlier: 4.312A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 122 " --> pdb=" O GLY A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 118 through 122' Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 517 through 527 Processing helix chain 'A' and resid 582 through 592 Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 619 through 634 Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.978A pdb=" N TYR A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 687 through 696 removed outlier: 4.253A pdb=" N ARG A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 694 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 749 removed outlier: 4.251A pdb=" N THR A 738 " --> pdb=" O HIS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 786 removed outlier: 3.744A pdb=" N GLU A 783 " --> pdb=" O ASN A 779 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 784 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 786 " --> pdb=" O VAL A 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.594A pdb=" N LEU B 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 517 through 527 Processing helix chain 'B' and resid 582 through 591 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 619 through 635 Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.634A pdb=" N TYR B 654 " --> pdb=" O ASP B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.935A pdb=" N ARG B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 694 " --> pdb=" O PHE B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 715 removed outlier: 3.541A pdb=" N SER B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 749 removed outlier: 4.304A pdb=" N THR B 738 " --> pdb=" O HIS B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 785 removed outlier: 4.646A pdb=" N GLU B 783 " --> pdb=" O ASN B 779 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS B 784 " --> pdb=" O PHE B 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 88 through 90 removed outlier: 3.535A pdb=" N SER J 90 " --> pdb=" O GLU J 93 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU J 93 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP J 106 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL J 103 " --> pdb=" O LEU J 116 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 112 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AA3, first strand: chain 'J' and resid 192 through 196 removed outlier: 6.095A pdb=" N TYR J 202 " --> pdb=" O ARG J 212 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ARG J 212 " --> pdb=" O TYR J 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'J' and resid 222 through 224 Processing sheet with id=AA6, first strand: chain 'J' and resid 264 through 266 Processing sheet with id=AA7, first strand: chain 'J' and resid 319 through 326 removed outlier: 5.596A pdb=" N ILE J 321 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU J 337 " --> pdb=" O ILE J 321 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET J 323 " --> pdb=" O THR J 335 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL J 343 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER J 344 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU J 361 " --> pdb=" O SER J 344 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU J 346 " --> pdb=" O LYS J 359 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL J 355 " --> pdb=" O ASP J 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 384 through 389 Processing sheet with id=AA9, first strand: chain 'J' and resid 425 through 432 removed outlier: 6.732A pdb=" N TYR J 439 " --> pdb=" O LEU J 429 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR J 431 " --> pdb=" O LYS J 437 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS J 437 " --> pdb=" O TYR J 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 478 through 481 removed outlier: 6.356A pdb=" N VAL J 502 " --> pdb=" O ASP J 513 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASP J 513 " --> pdb=" O VAL J 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 531 through 534 removed outlier: 3.795A pdb=" N LEU J 549 " --> pdb=" O VAL J 595 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL J 595 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS J 598 " --> pdb=" O VAL J 565 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR J 560 " --> pdb=" O ARG J 643 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N ALA J 645 " --> pdb=" O TYR J 560 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU J 562 " --> pdb=" O ALA J 645 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE J 647 " --> pdb=" O LEU J 562 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU J 564 " --> pdb=" O PHE J 647 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS J 673 " --> pdb=" O VAL J 644 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL J 646 " --> pdb=" O CYS J 673 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY J 674 " --> pdb=" O GLN J 721 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 537 through 539 Processing sheet with id=AB4, first strand: chain 'J' and resid 725 through 727 removed outlier: 3.516A pdb=" N HIS J 726 " --> pdb=" O GLN J 755 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR J 757 " --> pdb=" O HIS J 726 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 88 through 90 removed outlier: 3.682A pdb=" N GLU I 93 " --> pdb=" O SER I 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 103 through 107 removed outlier: 6.716A pdb=" N VAL I 103 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AB8, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.821A pdb=" N TYR I 202 " --> pdb=" O ARG I 212 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG I 212 " --> pdb=" O TYR I 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AC1, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AC2, first strand: chain 'I' and resid 263 through 266 Processing sheet with id=AC3, first strand: chain 'I' and resid 319 through 326 removed outlier: 5.688A pdb=" N ILE I 321 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU I 337 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL I 343 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER I 344 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU I 361 " --> pdb=" O SER I 344 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU I 346 " --> pdb=" O LYS I 359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 384 through 389 Processing sheet with id=AC5, first strand: chain 'I' and resid 425 through 432 removed outlier: 5.526A pdb=" N ILE I 428 " --> pdb=" O LEU I 441 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU I 441 " --> pdb=" O ILE I 428 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS I 437 " --> pdb=" O ASP I 432 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 478 through 481 removed outlier: 6.800A pdb=" N VAL I 502 " --> pdb=" O ASP I 513 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP I 513 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 531 through 532 removed outlier: 3.810A pdb=" N VAL I 595 " --> pdb=" O LEU I 549 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS I 598 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TYR I 560 " --> pdb=" O ARG I 643 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N ALA I 645 " --> pdb=" O TYR I 560 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU I 562 " --> pdb=" O ALA I 645 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE I 647 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU I 564 " --> pdb=" O PHE I 647 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 537 through 539 Processing sheet with id=AC9, first strand: chain 'I' and resid 722 through 727 removed outlier: 6.804A pdb=" N PHE I 722 " --> pdb=" O SER I 753 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLN I 755 " --> pdb=" O PHE I 722 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE I 724 " --> pdb=" O GLN I 755 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N TYR I 757 " --> pdb=" O ILE I 724 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS I 726 " --> pdb=" O TYR I 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.882A pdb=" N GLU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 106 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 103 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 112 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 129 through 132 Processing sheet with id=AD3, first strand: chain 'A' and resid 192 through 196 removed outlier: 6.092A pdb=" N TYR A 202 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ARG A 212 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=AD5, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=AD6, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AD7, first strand: chain 'A' and resid 319 through 326 removed outlier: 5.597A pdb=" N ILE A 321 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A 337 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 323 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 343 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER A 344 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 361 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 346 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 355 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 384 through 389 Processing sheet with id=AD9, first strand: chain 'A' and resid 425 through 432 removed outlier: 6.736A pdb=" N TYR A 439 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N TYR A 431 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS A 437 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 478 through 481 removed outlier: 6.421A pdb=" N VAL A 502 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP A 513 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 531 through 534 removed outlier: 3.769A pdb=" N LEU A 549 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 595 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS A 598 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N TYR A 560 " --> pdb=" O ARG A 643 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N ALA A 645 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 562 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE A 647 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 564 " --> pdb=" O PHE A 647 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS A 673 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 646 " --> pdb=" O CYS A 673 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 674 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AE4, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.519A pdb=" N HIS A 726 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 757 " --> pdb=" O HIS A 726 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.681A pdb=" N GLU B 93 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.717A pdb=" N VAL B 103 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 129 through 132 Processing sheet with id=AE8, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.825A pdb=" N TYR B 202 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG B 212 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 222 through 224 Processing sheet with id=AF1, first strand: chain 'B' and resid 222 through 224 Processing sheet with id=AF2, first strand: chain 'B' and resid 263 through 266 Processing sheet with id=AF3, first strand: chain 'B' and resid 319 through 326 removed outlier: 5.692A pdb=" N ILE B 321 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 337 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL B 343 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER B 344 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU B 361 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 346 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 384 through 389 Processing sheet with id=AF5, first strand: chain 'B' and resid 425 through 432 removed outlier: 5.489A pdb=" N ILE B 428 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 441 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS B 437 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 478 through 481 removed outlier: 6.797A pdb=" N VAL B 502 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP B 513 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.816A pdb=" N VAL B 595 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TYR B 560 " --> pdb=" O ARG B 643 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ALA B 645 " --> pdb=" O TYR B 560 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 562 " --> pdb=" O ALA B 645 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE B 647 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 564 " --> pdb=" O PHE B 647 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AF9, first strand: chain 'B' and resid 722 through 727 removed outlier: 6.793A pdb=" N PHE B 722 " --> pdb=" O SER B 753 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N GLN B 755 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE B 724 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N TYR B 757 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N HIS B 726 " --> pdb=" O TYR B 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 665 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.26 Time building geometry restraints manager: 10.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7640 1.34 - 1.46: 5798 1.46 - 1.58: 10538 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 24128 Sorted by residual: bond pdb=" C ILE I 162 " pdb=" N PRO I 163 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.43e+00 bond pdb=" C ILE B 162 " pdb=" N PRO B 163 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.34e+00 bond pdb=" C SER I 678 " pdb=" O SER I 678 " ideal model delta sigma weight residual 1.233 1.226 0.007 4.80e-03 4.34e+04 1.88e+00 bond pdb=" C ILE J 162 " pdb=" N PRO J 163 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 bond pdb=" C ILE A 162 " pdb=" N PRO A 163 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 ... (remaining 24123 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.16: 632 106.16 - 113.14: 12914 113.14 - 120.11: 8277 120.11 - 127.09: 10587 127.09 - 134.07: 314 Bond angle restraints: 32724 Sorted by residual: angle pdb=" C ILE I 659 " pdb=" N LEU I 660 " pdb=" CA LEU I 660 " ideal model delta sigma weight residual 123.21 117.95 5.26 1.19e+00 7.06e-01 1.96e+01 angle pdb=" C ILE B 659 " pdb=" N LEU B 660 " pdb=" CA LEU B 660 " ideal model delta sigma weight residual 123.21 118.10 5.11 1.19e+00 7.06e-01 1.85e+01 angle pdb=" N VAL J 710 " pdb=" CA VAL J 710 " pdb=" C VAL J 710 " ideal model delta sigma weight residual 112.98 108.96 4.02 1.25e+00 6.40e-01 1.04e+01 angle pdb=" N VAL A 710 " pdb=" CA VAL A 710 " pdb=" C VAL A 710 " ideal model delta sigma weight residual 112.98 108.96 4.02 1.25e+00 6.40e-01 1.03e+01 angle pdb=" N CYS J 468 " pdb=" CA CYS J 468 " pdb=" CB CYS J 468 " ideal model delta sigma weight residual 111.62 107.28 4.34 1.43e+00 4.89e-01 9.19e+00 ... (remaining 32719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12901 17.81 - 35.62: 1262 35.62 - 53.42: 220 53.42 - 71.23: 35 71.23 - 89.04: 26 Dihedral angle restraints: 14444 sinusoidal: 5888 harmonic: 8556 Sorted by residual: dihedral pdb=" CB CYS J 474 " pdb=" SG CYS J 474 " pdb=" SG CYS J 492 " pdb=" CB CYS J 492 " ideal model delta sinusoidal sigma weight residual -86.00 -23.15 -62.85 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 492 " pdb=" CB CYS A 492 " ideal model delta sinusoidal sigma weight residual -86.00 -23.26 -62.74 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS J 673 " pdb=" SG CYS J 673 " pdb=" SG CYS J 784 " pdb=" CB CYS J 784 " ideal model delta sinusoidal sigma weight residual 93.00 42.85 50.15 1 1.00e+01 1.00e-02 3.45e+01 ... (remaining 14441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2072 0.032 - 0.064: 952 0.064 - 0.096: 316 0.096 - 0.127: 177 0.127 - 0.159: 19 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CB ILE B 438 " pdb=" CA ILE B 438 " pdb=" CG1 ILE B 438 " pdb=" CG2 ILE B 438 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB ILE I 438 " pdb=" CA ILE I 438 " pdb=" CG1 ILE I 438 " pdb=" CG2 ILE I 438 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL B 158 " pdb=" N VAL B 158 " pdb=" C VAL B 158 " pdb=" CB VAL B 158 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 3533 not shown) Planarity restraints: 4216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 162 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 163 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 162 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO J 163 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO J 163 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 163 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 390 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO J 391 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO J 391 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 391 " -0.022 5.00e-02 4.00e+02 ... (remaining 4213 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1558 2.73 - 3.27: 25498 3.27 - 3.81: 40705 3.81 - 4.36: 49604 4.36 - 4.90: 82175 Nonbonded interactions: 199540 Sorted by model distance: nonbonded pdb=" O VAL A 69 " pdb=" OG SER A 590 " model vdw 2.182 2.440 nonbonded pdb=" O VAL J 69 " pdb=" OG SER J 590 " model vdw 2.184 2.440 nonbonded pdb=" OG1 THR B 475 " pdb=" OE1 GLU B 577 " model vdw 2.194 2.440 nonbonded pdb=" OG1 THR I 475 " pdb=" OE1 GLU I 577 " model vdw 2.195 2.440 nonbonded pdb=" OD2 ASP I 640 " pdb=" OG1 THR I 642 " model vdw 2.202 2.440 ... (remaining 199535 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' selection = chain 'B' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.640 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 61.580 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 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 : 0.003 0.036 24128 Z= 0.208 Angle : 0.626 8.475 32724 Z= 0.339 Chirality : 0.045 0.159 3536 Planarity : 0.004 0.042 4216 Dihedral : 14.518 89.041 8908 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.11 (0.15), residues: 2908 helix: -0.64 (0.25), residues: 422 sheet: -0.87 (0.18), residues: 836 loop : -1.93 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 229 HIS 0.005 0.001 HIS A 762 PHE 0.018 0.002 PHE J 75 TYR 0.023 0.001 TYR I 686 ARG 0.003 0.000 ARG J 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 2.816 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: J 95 ILE cc_start: 0.6301 (mm) cc_final: 0.5978 (mm) REVERT: J 117 ILE cc_start: 0.6027 (mm) cc_final: 0.5660 (mm) REVERT: J 129 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7617 (ttp-110) REVERT: J 309 MET cc_start: 0.7138 (tpt) cc_final: 0.6936 (tpp) REVERT: J 369 HIS cc_start: 0.6339 (t-170) cc_final: 0.6002 (t-170) REVERT: J 399 TYR cc_start: 0.4479 (m-80) cc_final: 0.4137 (m-80) REVERT: J 483 HIS cc_start: 0.4973 (m-70) cc_final: 0.4649 (m90) REVERT: J 485 MET cc_start: 0.4462 (mpp) cc_final: 0.4186 (mpp) REVERT: J 535 ARG cc_start: 0.6055 (ttm110) cc_final: 0.4861 (tmt-80) REVERT: J 594 VAL cc_start: 0.5820 (m) cc_final: 0.5602 (m) REVERT: J 595 VAL cc_start: 0.6885 (p) cc_final: 0.6630 (p) REVERT: J 630 VAL cc_start: 0.6698 (t) cc_final: 0.6431 (t) REVERT: J 673 CYS cc_start: 0.1887 (p) cc_final: 0.1667 (p) REVERT: J 685 LEU cc_start: 0.8253 (mt) cc_final: 0.7950 (mp) REVERT: J 703 ARG cc_start: 0.7115 (ttp-170) cc_final: 0.6772 (ttm170) REVERT: J 732 LYS cc_start: 0.8078 (tptp) cc_final: 0.7757 (mmtt) REVERT: J 744 GLN cc_start: 0.7658 (tp40) cc_final: 0.7309 (tm-30) REVERT: I 77 GLU cc_start: 0.7012 (tp30) cc_final: 0.6628 (mm-30) REVERT: I 164 HIS cc_start: 0.5613 (p-80) cc_final: 0.5329 (p90) REVERT: I 304 HIS cc_start: 0.5970 (t-170) cc_final: 0.5670 (t70) REVERT: I 308 MET cc_start: 0.8058 (mpp) cc_final: 0.7080 (mpp) REVERT: I 546 MET cc_start: 0.8112 (tmm) cc_final: 0.7762 (tmm) REVERT: I 657 THR cc_start: 0.8657 (p) cc_final: 0.8424 (p) REVERT: I 778 ILE cc_start: 0.8242 (mm) cc_final: 0.7986 (mm) REVERT: A 95 ILE cc_start: 0.6268 (mm) cc_final: 0.5942 (mm) REVERT: A 117 ILE cc_start: 0.6017 (mm) cc_final: 0.5653 (mm) REVERT: A 129 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7615 (ttp-110) REVERT: A 309 MET cc_start: 0.7125 (tpt) cc_final: 0.6923 (tpp) REVERT: A 369 HIS cc_start: 0.6338 (t-170) cc_final: 0.5991 (t-170) REVERT: A 399 TYR cc_start: 0.4481 (m-80) cc_final: 0.4140 (m-80) REVERT: A 483 HIS cc_start: 0.4977 (m-70) cc_final: 0.4592 (m90) REVERT: A 485 MET cc_start: 0.4756 (mpp) cc_final: 0.4311 (mpp) REVERT: A 535 ARG cc_start: 0.6111 (ttm110) cc_final: 0.4998 (tmt-80) REVERT: A 594 VAL cc_start: 0.5857 (m) cc_final: 0.5648 (p) REVERT: A 630 VAL cc_start: 0.6688 (t) cc_final: 0.6413 (t) REVERT: A 685 LEU cc_start: 0.8179 (mt) cc_final: 0.7853 (mp) REVERT: A 703 ARG cc_start: 0.7195 (ttp-170) cc_final: 0.6859 (ttm170) REVERT: A 732 LYS cc_start: 0.8070 (tptp) cc_final: 0.7758 (mmtt) REVERT: A 744 GLN cc_start: 0.7498 (tp40) cc_final: 0.7264 (tm-30) REVERT: B 77 GLU cc_start: 0.7029 (tp30) cc_final: 0.6641 (mm-30) REVERT: B 164 HIS cc_start: 0.5558 (p-80) cc_final: 0.5292 (p90) REVERT: B 308 MET cc_start: 0.8058 (mpp) cc_final: 0.7083 (mpp) REVERT: B 546 MET cc_start: 0.8198 (tmm) cc_final: 0.7881 (tmm) REVERT: B 657 THR cc_start: 0.8647 (p) cc_final: 0.8413 (p) outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 0.3996 time to fit residues: 211.4531 Evaluate side-chains 186 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 116 optimal weight: 0.1980 chunk 225 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 190 GLN J 451 GLN ** J 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 591 HIS ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 451 GLN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24128 Z= 0.289 Angle : 0.694 7.396 32724 Z= 0.365 Chirality : 0.047 0.149 3536 Planarity : 0.005 0.043 4216 Dihedral : 5.415 32.784 3208 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 1.69 % Allowed : 10.52 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2908 helix: -0.86 (0.24), residues: 440 sheet: -1.04 (0.18), residues: 824 loop : -1.99 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 367 HIS 0.012 0.002 HIS A 205 PHE 0.028 0.003 PHE A 722 TYR 0.020 0.002 TYR J 320 ARG 0.007 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 192 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5935 (mm) cc_final: 0.5544 (mm) REVERT: J 129 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7801 (ttp-110) REVERT: J 323 MET cc_start: 0.6135 (tmm) cc_final: 0.5066 (tmm) REVERT: J 369 HIS cc_start: 0.6537 (t-170) cc_final: 0.5963 (t-170) REVERT: J 485 MET cc_start: 0.4510 (mpp) cc_final: 0.4168 (mpp) REVERT: J 535 ARG cc_start: 0.5935 (ttm110) cc_final: 0.4677 (tmt-80) REVERT: J 685 LEU cc_start: 0.8013 (mt) cc_final: 0.7675 (mp) REVERT: J 744 GLN cc_start: 0.7359 (tp40) cc_final: 0.6946 (tm-30) REVERT: I 77 GLU cc_start: 0.7139 (tp30) cc_final: 0.6653 (mm-30) REVERT: I 143 TYR cc_start: 0.5349 (p90) cc_final: 0.4903 (p90) REVERT: I 546 MET cc_start: 0.7851 (tmm) cc_final: 0.7241 (tmm) REVERT: I 562 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6137 (tp) REVERT: I 627 MET cc_start: 0.7280 (tpt) cc_final: 0.6786 (ttp) REVERT: A 117 ILE cc_start: 0.5925 (mm) cc_final: 0.5528 (mm) REVERT: A 129 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7790 (ttp-110) REVERT: A 323 MET cc_start: 0.6153 (tmm) cc_final: 0.5125 (tmm) REVERT: A 369 HIS cc_start: 0.6537 (t-170) cc_final: 0.5947 (t-170) REVERT: A 535 ARG cc_start: 0.5764 (ttm110) cc_final: 0.4477 (tmt-80) REVERT: A 685 LEU cc_start: 0.7946 (mt) cc_final: 0.7703 (mp) REVERT: A 744 GLN cc_start: 0.7387 (tp40) cc_final: 0.6995 (tm-30) REVERT: B 77 GLU cc_start: 0.7169 (tp30) cc_final: 0.6696 (mm-30) REVERT: B 143 TYR cc_start: 0.5382 (p90) cc_final: 0.4933 (p90) REVERT: B 546 MET cc_start: 0.7979 (tmm) cc_final: 0.7249 (tmm) REVERT: B 562 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6145 (tp) REVERT: B 627 MET cc_start: 0.7234 (tpt) cc_final: 0.6777 (ttp) outliers start: 44 outliers final: 29 residues processed: 229 average time/residue: 0.3490 time to fit residues: 126.2985 Evaluate side-chains 186 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 513 ASP Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 262 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 483 HIS J 504 ASN J 744 GLN ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 HIS ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24128 Z= 0.277 Angle : 0.659 8.269 32724 Z= 0.349 Chirality : 0.046 0.141 3536 Planarity : 0.005 0.046 4216 Dihedral : 5.436 35.924 3208 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 3.20 % Allowed : 13.25 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.43 (0.15), residues: 2908 helix: -0.85 (0.23), residues: 450 sheet: -1.11 (0.19), residues: 794 loop : -2.14 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 336 HIS 0.007 0.001 HIS I 205 PHE 0.024 0.002 PHE I 722 TYR 0.032 0.002 TYR I 431 ARG 0.006 0.001 ARG J 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 168 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5662 (mm) cc_final: 0.5207 (mm) REVERT: J 129 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7744 (ttp-110) REVERT: J 323 MET cc_start: 0.6175 (tmm) cc_final: 0.5571 (tmm) REVERT: J 369 HIS cc_start: 0.6742 (t-170) cc_final: 0.6204 (t-170) REVERT: J 387 ILE cc_start: 0.4103 (OUTLIER) cc_final: 0.3687 (mt) REVERT: J 744 GLN cc_start: 0.7173 (tp-100) cc_final: 0.6843 (tm-30) REVERT: I 143 TYR cc_start: 0.5342 (p90) cc_final: 0.4918 (p90) REVERT: I 308 MET cc_start: 0.7681 (mpp) cc_final: 0.7323 (mpp) REVERT: I 316 MET cc_start: 0.5541 (tpt) cc_final: 0.5212 (tpt) REVERT: I 627 MET cc_start: 0.7371 (tpt) cc_final: 0.6809 (ttp) REVERT: A 117 ILE cc_start: 0.5669 (mm) cc_final: 0.5185 (mm) REVERT: A 129 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7737 (ttp-110) REVERT: A 323 MET cc_start: 0.6093 (tmm) cc_final: 0.5472 (tmm) REVERT: A 369 HIS cc_start: 0.6733 (t-170) cc_final: 0.6191 (t-170) REVERT: A 387 ILE cc_start: 0.4134 (OUTLIER) cc_final: 0.3713 (mt) REVERT: A 744 GLN cc_start: 0.7101 (tp40) cc_final: 0.6768 (tm-30) REVERT: B 143 TYR cc_start: 0.5375 (p90) cc_final: 0.4946 (p90) REVERT: B 308 MET cc_start: 0.7675 (mpp) cc_final: 0.7265 (mpp) REVERT: B 316 MET cc_start: 0.5651 (tpt) cc_final: 0.5311 (tpt) REVERT: B 627 MET cc_start: 0.7335 (tpt) cc_final: 0.6805 (ttp) REVERT: B 641 ARG cc_start: 0.5152 (tpt90) cc_final: 0.4805 (mmt-90) outliers start: 83 outliers final: 52 residues processed: 234 average time/residue: 0.3381 time to fit residues: 127.9125 Evaluate side-chains 198 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 144 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 525 ASN Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 630 VAL Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 673 CYS Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 504 ASN Chi-restraints excluded: chain I residue 513 ASP Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 262 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 451 GLN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24128 Z= 0.227 Angle : 0.615 8.162 32724 Z= 0.326 Chirality : 0.045 0.138 3536 Planarity : 0.004 0.044 4216 Dihedral : 5.332 35.308 3208 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 3.89 % Allowed : 15.64 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.39 (0.15), residues: 2908 helix: -0.80 (0.23), residues: 452 sheet: -1.07 (0.19), residues: 782 loop : -2.13 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 336 HIS 0.005 0.001 HIS B 591 PHE 0.018 0.002 PHE B 722 TYR 0.015 0.002 TYR I 431 ARG 0.005 0.000 ARG J 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 162 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5762 (mm) cc_final: 0.5343 (mm) REVERT: J 129 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7824 (ttp-110) REVERT: J 323 MET cc_start: 0.6013 (tmm) cc_final: 0.5381 (tmm) REVERT: J 369 HIS cc_start: 0.6727 (t-170) cc_final: 0.6128 (t-170) REVERT: J 744 GLN cc_start: 0.7042 (tp-100) cc_final: 0.6750 (tm-30) REVERT: I 59 GLU cc_start: 0.0634 (OUTLIER) cc_final: -0.0059 (pm20) REVERT: I 143 TYR cc_start: 0.5450 (p90) cc_final: 0.4948 (p90) REVERT: I 308 MET cc_start: 0.7486 (mpp) cc_final: 0.7081 (mpp) REVERT: I 316 MET cc_start: 0.5851 (tpt) cc_final: 0.5494 (tpt) REVERT: I 627 MET cc_start: 0.7362 (tpt) cc_final: 0.6819 (ttp) REVERT: A 117 ILE cc_start: 0.5752 (mm) cc_final: 0.5329 (mm) REVERT: A 129 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7818 (ttp-110) REVERT: A 323 MET cc_start: 0.5998 (tmm) cc_final: 0.5371 (tmm) REVERT: A 369 HIS cc_start: 0.6719 (t-170) cc_final: 0.6107 (t-170) REVERT: A 744 GLN cc_start: 0.6959 (tp-100) cc_final: 0.6725 (tm-30) REVERT: B 143 TYR cc_start: 0.5492 (p90) cc_final: 0.4988 (p90) REVERT: B 308 MET cc_start: 0.7485 (mpp) cc_final: 0.7092 (mpp) REVERT: B 316 MET cc_start: 0.5859 (tpt) cc_final: 0.5493 (tpt) REVERT: B 627 MET cc_start: 0.7316 (tpt) cc_final: 0.6924 (ttp) REVERT: B 641 ARG cc_start: 0.5337 (tpt90) cc_final: 0.5033 (mmt-90) outliers start: 101 outliers final: 60 residues processed: 252 average time/residue: 0.3199 time to fit residues: 131.3368 Evaluate side-chains 209 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 148 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 673 CYS Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 504 ASN Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 513 ASP Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 30.0000 chunk 158 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 237 optimal weight: 0.3980 chunk 192 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 0.0370 chunk 249 optimal weight: 7.9990 chunk 70 optimal weight: 0.0270 overall best weight: 2.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 HIS J 451 GLN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24128 Z= 0.248 Angle : 0.632 8.121 32724 Z= 0.334 Chirality : 0.045 0.139 3536 Planarity : 0.004 0.049 4216 Dihedral : 5.370 37.070 3208 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 4.24 % Allowed : 17.49 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.41 (0.15), residues: 2908 helix: -0.82 (0.23), residues: 452 sheet: -1.12 (0.19), residues: 796 loop : -2.13 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 367 HIS 0.005 0.001 HIS B 483 PHE 0.019 0.002 PHE I 722 TYR 0.038 0.002 TYR B 431 ARG 0.005 0.000 ARG J 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 163 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5656 (mm) cc_final: 0.5193 (mm) REVERT: J 129 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7902 (ttp-110) REVERT: J 323 MET cc_start: 0.6082 (tmm) cc_final: 0.5422 (tmm) REVERT: J 369 HIS cc_start: 0.6805 (t-170) cc_final: 0.6187 (t-170) REVERT: J 744 GLN cc_start: 0.6987 (tp-100) cc_final: 0.6730 (tm-30) REVERT: J 783 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6467 (mp0) REVERT: I 143 TYR cc_start: 0.5448 (p90) cc_final: 0.4895 (p90) REVERT: I 308 MET cc_start: 0.7551 (mpp) cc_final: 0.7143 (mpp) REVERT: I 316 MET cc_start: 0.5774 (tpt) cc_final: 0.5324 (tpp) REVERT: I 562 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5717 (tp) REVERT: I 627 MET cc_start: 0.7340 (tpt) cc_final: 0.6914 (ttp) REVERT: A 117 ILE cc_start: 0.5627 (mm) cc_final: 0.5161 (mm) REVERT: A 129 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7899 (ttp-110) REVERT: A 323 MET cc_start: 0.6078 (tmm) cc_final: 0.5427 (tmm) REVERT: A 369 HIS cc_start: 0.6807 (t-170) cc_final: 0.6167 (t-170) REVERT: A 387 ILE cc_start: 0.4381 (OUTLIER) cc_final: 0.4012 (mt) REVERT: A 744 GLN cc_start: 0.6911 (tp-100) cc_final: 0.6700 (tm-30) REVERT: B 143 TYR cc_start: 0.5493 (p90) cc_final: 0.4938 (p90) REVERT: B 308 MET cc_start: 0.7584 (mpp) cc_final: 0.7113 (mpp) REVERT: B 316 MET cc_start: 0.5773 (tpt) cc_final: 0.5322 (tpp) REVERT: B 562 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5825 (tp) REVERT: B 591 HIS cc_start: 0.7290 (m90) cc_final: 0.6861 (m-70) REVERT: B 627 MET cc_start: 0.7385 (tpt) cc_final: 0.6810 (ttp) REVERT: B 641 ARG cc_start: 0.5502 (tpt90) cc_final: 0.4867 (mmm160) outliers start: 110 outliers final: 70 residues processed: 262 average time/residue: 0.3278 time to fit residues: 139.3489 Evaluate side-chains 225 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 151 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 504 ASN Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 673 CYS Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 738 THR Chi-restraints excluded: chain J residue 783 GLU Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 504 ASN Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 513 ASP Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.0070 chunk 250 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 278 optimal weight: 0.0570 chunk 231 optimal weight: 0.0000 chunk 129 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 451 GLN ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 744 GLN ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24128 Z= 0.225 Angle : 0.620 8.034 32724 Z= 0.327 Chirality : 0.045 0.225 3536 Planarity : 0.004 0.042 4216 Dihedral : 5.334 36.293 3208 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 4.35 % Allowed : 18.07 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.41 (0.15), residues: 2908 helix: -0.65 (0.23), residues: 440 sheet: -1.13 (0.19), residues: 812 loop : -2.17 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 336 HIS 0.005 0.001 HIS B 591 PHE 0.017 0.002 PHE J 75 TYR 0.017 0.002 TYR B 431 ARG 0.005 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 166 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5617 (mm) cc_final: 0.5162 (mm) REVERT: J 129 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.7822 (mmm160) REVERT: J 130 TYR cc_start: 0.5041 (p90) cc_final: 0.4769 (p90) REVERT: J 323 MET cc_start: 0.6104 (tmm) cc_final: 0.5447 (tmm) REVERT: J 369 HIS cc_start: 0.6767 (t-170) cc_final: 0.6142 (t-170) REVERT: J 387 ILE cc_start: 0.4326 (OUTLIER) cc_final: 0.3986 (mt) REVERT: J 744 GLN cc_start: 0.6921 (tp-100) cc_final: 0.6698 (tm-30) REVERT: J 783 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: I 308 MET cc_start: 0.7561 (mpp) cc_final: 0.7159 (mpp) REVERT: I 316 MET cc_start: 0.5764 (tpt) cc_final: 0.5354 (tpp) REVERT: I 562 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5848 (tp) REVERT: I 627 MET cc_start: 0.7373 (tpt) cc_final: 0.6827 (ttp) REVERT: I 698 HIS cc_start: 0.5718 (OUTLIER) cc_final: 0.5207 (t70) REVERT: A 117 ILE cc_start: 0.5591 (mm) cc_final: 0.5135 (mm) REVERT: A 129 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7825 (mmm160) REVERT: A 130 TYR cc_start: 0.5073 (p90) cc_final: 0.4795 (p90) REVERT: A 323 MET cc_start: 0.6207 (tmm) cc_final: 0.5601 (tmm) REVERT: A 369 HIS cc_start: 0.6761 (t-170) cc_final: 0.6157 (t-170) REVERT: A 744 GLN cc_start: 0.6886 (tp-100) cc_final: 0.6665 (tm-30) REVERT: B 308 MET cc_start: 0.7570 (mpp) cc_final: 0.7173 (mpp) REVERT: B 316 MET cc_start: 0.5760 (tpt) cc_final: 0.5344 (tpp) REVERT: B 562 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5809 (tp) REVERT: B 627 MET cc_start: 0.7302 (tpt) cc_final: 0.6845 (ttp) REVERT: B 641 ARG cc_start: 0.5476 (tpt90) cc_final: 0.4655 (mmm-85) REVERT: B 698 HIS cc_start: 0.5700 (OUTLIER) cc_final: 0.5206 (t70) outliers start: 113 outliers final: 70 residues processed: 267 average time/residue: 0.3241 time to fit residues: 142.0519 Evaluate side-chains 226 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 150 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 673 CYS Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain J residue 783 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 504 ASN Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 513 ASP Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 155 optimal weight: 0.2980 chunk 277 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 473 ASN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 HIS ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24128 Z= 0.176 Angle : 0.593 7.441 32724 Z= 0.308 Chirality : 0.045 0.245 3536 Planarity : 0.004 0.041 4216 Dihedral : 5.102 32.136 3208 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 2.89 % Allowed : 19.03 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2908 helix: -0.49 (0.23), residues: 434 sheet: -1.06 (0.19), residues: 806 loop : -2.08 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 367 HIS 0.003 0.001 HIS B 591 PHE 0.021 0.001 PHE A 386 TYR 0.018 0.001 TYR A 453 ARG 0.003 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 164 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5819 (mm) cc_final: 0.5422 (mm) REVERT: J 129 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7681 (ttp80) REVERT: J 130 TYR cc_start: 0.5089 (p90) cc_final: 0.4686 (p90) REVERT: J 153 TYR cc_start: 0.6514 (p90) cc_final: 0.6053 (p90) REVERT: J 323 MET cc_start: 0.5971 (tmm) cc_final: 0.5291 (tmm) REVERT: J 744 GLN cc_start: 0.6925 (tp-100) cc_final: 0.6583 (tm-30) REVERT: I 143 TYR cc_start: 0.5091 (p90) cc_final: 0.4636 (p90) REVERT: I 316 MET cc_start: 0.5620 (tpt) cc_final: 0.5206 (tpp) REVERT: I 529 MET cc_start: 0.8106 (tmm) cc_final: 0.7670 (tmm) REVERT: I 546 MET cc_start: 0.7911 (tmm) cc_final: 0.7192 (tmm) REVERT: I 627 MET cc_start: 0.7299 (tpt) cc_final: 0.6825 (ttp) REVERT: I 698 HIS cc_start: 0.5680 (OUTLIER) cc_final: 0.5238 (t70) REVERT: A 117 ILE cc_start: 0.5801 (mm) cc_final: 0.5376 (mm) REVERT: A 129 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7680 (ttp80) REVERT: A 130 TYR cc_start: 0.5070 (p90) cc_final: 0.4681 (p90) REVERT: A 323 MET cc_start: 0.5969 (tmm) cc_final: 0.5291 (tmm) REVERT: A 744 GLN cc_start: 0.6846 (tp-100) cc_final: 0.6568 (tm-30) REVERT: A 783 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5519 (mp0) REVERT: B 143 TYR cc_start: 0.5131 (p90) cc_final: 0.4684 (p90) REVERT: B 316 MET cc_start: 0.5616 (tpt) cc_final: 0.5197 (tpp) REVERT: B 529 MET cc_start: 0.8119 (tmm) cc_final: 0.7694 (tmm) REVERT: B 627 MET cc_start: 0.7279 (tpt) cc_final: 0.6864 (ttp) REVERT: B 641 ARG cc_start: 0.5405 (tpt90) cc_final: 0.4779 (mmm160) outliers start: 75 outliers final: 56 residues processed: 231 average time/residue: 0.3357 time to fit residues: 124.7789 Evaluate side-chains 212 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 154 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 504 ASN Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 673 CYS Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 504 ASN Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 513 ASP Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 165 optimal weight: 0.0770 chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 218 optimal weight: 0.0570 overall best weight: 3.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24128 Z= 0.267 Angle : 0.654 8.780 32724 Z= 0.344 Chirality : 0.046 0.198 3536 Planarity : 0.004 0.042 4216 Dihedral : 5.343 37.045 3208 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 3.62 % Allowed : 19.14 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.41 (0.15), residues: 2908 helix: -0.68 (0.23), residues: 436 sheet: -1.07 (0.19), residues: 784 loop : -2.19 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 367 HIS 0.006 0.001 HIS I 483 PHE 0.021 0.002 PHE A 386 TYR 0.016 0.002 TYR I 253 ARG 0.004 0.001 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 156 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5655 (mm) cc_final: 0.5210 (mm) REVERT: J 323 MET cc_start: 0.6143 (tmm) cc_final: 0.5544 (tmm) REVERT: J 369 HIS cc_start: 0.6905 (t-170) cc_final: 0.6385 (t-170) REVERT: J 744 GLN cc_start: 0.6697 (tp-100) cc_final: 0.6465 (tm-30) REVERT: I 143 TYR cc_start: 0.5272 (p90) cc_final: 0.4773 (p90) REVERT: I 308 MET cc_start: 0.7339 (mpp) cc_final: 0.7134 (mpp) REVERT: I 316 MET cc_start: 0.5703 (tpt) cc_final: 0.5255 (tpp) REVERT: I 546 MET cc_start: 0.7950 (tmm) cc_final: 0.7123 (tmm) REVERT: I 562 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5764 (tp) REVERT: I 627 MET cc_start: 0.7364 (tpt) cc_final: 0.6853 (ttp) REVERT: I 698 HIS cc_start: 0.5698 (OUTLIER) cc_final: 0.5134 (t70) REVERT: A 117 ILE cc_start: 0.5622 (mm) cc_final: 0.5176 (mm) REVERT: A 323 MET cc_start: 0.6142 (tmm) cc_final: 0.5545 (tmm) REVERT: A 369 HIS cc_start: 0.6803 (t-170) cc_final: 0.6272 (t-170) REVERT: A 387 ILE cc_start: 0.4375 (OUTLIER) cc_final: 0.4048 (mt) REVERT: A 744 GLN cc_start: 0.6754 (tp-100) cc_final: 0.6486 (tm-30) REVERT: A 783 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5578 (mp0) REVERT: B 143 TYR cc_start: 0.5308 (p90) cc_final: 0.4817 (p90) REVERT: B 316 MET cc_start: 0.5693 (tpt) cc_final: 0.5255 (tpp) REVERT: B 431 TYR cc_start: 0.3778 (t80) cc_final: 0.3490 (t80) REVERT: B 546 MET cc_start: 0.7792 (tmm) cc_final: 0.7050 (tmm) REVERT: B 562 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5839 (tp) REVERT: B 627 MET cc_start: 0.7257 (tpt) cc_final: 0.6818 (ttp) REVERT: B 641 ARG cc_start: 0.5571 (tpt90) cc_final: 0.4786 (mmm-85) REVERT: B 698 HIS cc_start: 0.5770 (OUTLIER) cc_final: 0.5197 (t70) outliers start: 94 outliers final: 74 residues processed: 240 average time/residue: 0.3278 time to fit residues: 128.5558 Evaluate side-chains 225 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 145 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 261 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 504 ASN Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 673 CYS Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 320 TYR Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 504 ASN Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 513 ASP Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 710 VAL Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 257 optimal weight: 7.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 HIS ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS B 606 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24128 Z= 0.324 Angle : 0.697 7.940 32724 Z= 0.369 Chirality : 0.047 0.170 3536 Planarity : 0.005 0.046 4216 Dihedral : 5.696 41.125 3208 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.93 % Favored : 88.03 % Rotamer: Outliers : 3.78 % Allowed : 19.38 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.57 (0.15), residues: 2908 helix: -0.99 (0.23), residues: 448 sheet: -1.15 (0.19), residues: 788 loop : -2.26 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 367 HIS 0.010 0.002 HIS A 205 PHE 0.026 0.003 PHE I 722 TYR 0.020 0.002 TYR I 253 ARG 0.006 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 153 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5697 (mm) cc_final: 0.5257 (mm) REVERT: J 323 MET cc_start: 0.6210 (tmm) cc_final: 0.5073 (tmm) REVERT: J 744 GLN cc_start: 0.6851 (tp-100) cc_final: 0.6594 (tm-30) REVERT: I 143 TYR cc_start: 0.5348 (p90) cc_final: 0.4858 (p90) REVERT: I 308 MET cc_start: 0.7366 (mpp) cc_final: 0.7130 (mpp) REVERT: I 316 MET cc_start: 0.5642 (tpt) cc_final: 0.5214 (tpp) REVERT: I 546 MET cc_start: 0.7960 (tmm) cc_final: 0.7059 (tmm) REVERT: I 562 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5766 (tp) REVERT: I 627 MET cc_start: 0.7359 (tpt) cc_final: 0.6848 (ttp) REVERT: I 698 HIS cc_start: 0.5754 (OUTLIER) cc_final: 0.5165 (t70) REVERT: A 117 ILE cc_start: 0.5657 (mm) cc_final: 0.5215 (mm) REVERT: A 153 TYR cc_start: 0.6153 (OUTLIER) cc_final: 0.5255 (p90) REVERT: A 323 MET cc_start: 0.6202 (tmm) cc_final: 0.5080 (tmm) REVERT: A 387 ILE cc_start: 0.4375 (OUTLIER) cc_final: 0.3949 (mt) REVERT: A 744 GLN cc_start: 0.6863 (tp-100) cc_final: 0.6649 (tm-30) REVERT: A 783 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5804 (mp0) REVERT: B 59 GLU cc_start: 0.1074 (OUTLIER) cc_final: 0.0769 (pt0) REVERT: B 143 TYR cc_start: 0.5387 (p90) cc_final: 0.4898 (p90) REVERT: B 308 MET cc_start: 0.7370 (mpp) cc_final: 0.7135 (mpp) REVERT: B 316 MET cc_start: 0.5601 (tpt) cc_final: 0.5163 (tpp) REVERT: B 546 MET cc_start: 0.7879 (tmm) cc_final: 0.6922 (tmm) REVERT: B 562 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5728 (tp) REVERT: B 627 MET cc_start: 0.7277 (tpt) cc_final: 0.6835 (ttp) REVERT: B 641 ARG cc_start: 0.5533 (tpt90) cc_final: 0.5023 (mmm-85) REVERT: B 698 HIS cc_start: 0.5727 (OUTLIER) cc_final: 0.5021 (t70) outliers start: 98 outliers final: 72 residues processed: 241 average time/residue: 0.3189 time to fit residues: 127.1569 Evaluate side-chains 227 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 147 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain J residue 261 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 457 THR Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 504 ASN Chi-restraints excluded: chain J residue 507 ASP Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 673 CYS Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain J residue 728 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 458 VAL Chi-restraints excluded: chain I residue 504 ASN Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 513 ASP Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 567 ASP Chi-restraints excluded: chain I residue 691 SER Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 746 ILE Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 776 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 776 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 264 optimal weight: 20.0000 chunk 228 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24128 Z= 0.178 Angle : 0.611 10.882 32724 Z= 0.317 Chirality : 0.045 0.162 3536 Planarity : 0.004 0.041 4216 Dihedral : 5.239 34.098 3208 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.20 % Allowed : 20.84 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.35 (0.15), residues: 2908 helix: -0.57 (0.23), residues: 442 sheet: -1.18 (0.18), residues: 820 loop : -2.10 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 367 HIS 0.005 0.001 HIS B 591 PHE 0.022 0.001 PHE A 386 TYR 0.027 0.001 TYR B 431 ARG 0.005 0.000 ARG J 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 167 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 117 ILE cc_start: 0.5954 (mm) cc_final: 0.5546 (mm) REVERT: J 323 MET cc_start: 0.6021 (tmm) cc_final: 0.5358 (tmm) REVERT: J 744 GLN cc_start: 0.6909 (tp-100) cc_final: 0.6703 (tm-30) REVERT: I 143 TYR cc_start: 0.5504 (p90) cc_final: 0.5069 (p90) REVERT: I 316 MET cc_start: 0.5545 (tpt) cc_final: 0.5153 (tpp) REVERT: I 546 MET cc_start: 0.7739 (tmm) cc_final: 0.7281 (tmm) REVERT: I 627 MET cc_start: 0.7265 (tpt) cc_final: 0.6782 (ttp) REVERT: I 698 HIS cc_start: 0.5742 (OUTLIER) cc_final: 0.5180 (t70) REVERT: A 117 ILE cc_start: 0.5781 (mm) cc_final: 0.5348 (mm) REVERT: A 153 TYR cc_start: 0.6164 (OUTLIER) cc_final: 0.5389 (p90) REVERT: A 323 MET cc_start: 0.6009 (tmm) cc_final: 0.5392 (tmm) REVERT: A 744 GLN cc_start: 0.6946 (tp-100) cc_final: 0.6745 (tm-30) REVERT: A 783 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5735 (mp0) REVERT: B 143 TYR cc_start: 0.5544 (p90) cc_final: 0.5113 (p90) REVERT: B 316 MET cc_start: 0.5549 (tpt) cc_final: 0.5155 (tpp) REVERT: B 546 MET cc_start: 0.7665 (tmm) cc_final: 0.7363 (tmm) REVERT: B 627 MET cc_start: 0.7151 (tpt) cc_final: 0.6694 (ttp) REVERT: B 641 ARG cc_start: 0.5441 (tpt90) cc_final: 0.5026 (mmt-90) REVERT: B 698 HIS cc_start: 0.5744 (OUTLIER) cc_final: 0.5106 (t70) outliers start: 57 outliers final: 47 residues processed: 218 average time/residue: 0.3284 time to fit residues: 116.1825 Evaluate side-chains 201 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 150 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 504 ASN Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 622 GLU Chi-restraints excluded: chain J residue 656 SER Chi-restraints excluded: chain J residue 673 CYS Chi-restraints excluded: chain J residue 680 ILE Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 504 ASN Chi-restraints excluded: chain I residue 511 MET Chi-restraints excluded: chain I residue 513 ASP Chi-restraints excluded: chain I residue 562 LEU Chi-restraints excluded: chain I residue 566 VAL Chi-restraints excluded: chain I residue 698 HIS Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 6.9990 chunk 243 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 210 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 63 optimal weight: 0.0000 chunk 228 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 HIS ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.084231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.069717 restraints weight = 112438.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.069444 restraints weight = 85132.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.069905 restraints weight = 74282.299| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24128 Z= 0.185 Angle : 0.600 10.541 32724 Z= 0.313 Chirality : 0.045 0.312 3536 Planarity : 0.004 0.041 4216 Dihedral : 5.142 32.224 3208 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 2.39 % Allowed : 20.69 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.29 (0.15), residues: 2908 helix: -0.41 (0.24), residues: 442 sheet: -1.12 (0.18), residues: 812 loop : -2.09 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 367 HIS 0.011 0.001 HIS J 772 PHE 0.022 0.002 PHE A 386 TYR 0.045 0.001 TYR J 453 ARG 0.004 0.000 ARG J 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3967.00 seconds wall clock time: 74 minutes 52.57 seconds (4492.57 seconds total)