Starting phenix.real_space_refine on Thu Mar 21 21:00:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9m_8788/03_2024/5w9m_8788.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9m_8788/03_2024/5w9m_8788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9m_8788/03_2024/5w9m_8788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9m_8788/03_2024/5w9m_8788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9m_8788/03_2024/5w9m_8788.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9m_8788/03_2024/5w9m_8788.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 19751 2.51 5 N 5166 2.21 5 O 6038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J GLU 536": "OE1" <-> "OE2" Residue "J TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31126 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3496 Classifications: {'peptide': 457} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 431} Chain breaks: 2 Chain: "G" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 3, 'PTRANS': 36, 'TRANS': 686} Chain: "F" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "J" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Time building chain proxies: 16.38, per 1000 atoms: 0.53 Number of scatterers: 31126 At special positions: 0 Unit cell: (155.04, 154.02, 217.26, 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 171 16.00 O 6038 8.00 N 5166 7.00 C 19751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=1.88 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.02 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.11 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.05 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.03 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.03 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.11 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.03 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.00 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.02 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.03 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.05 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.13 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.14 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=1.98 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 195 " distance=2.06 Simple disulfide: pdb=" SG CYS E 176 " - pdb=" SG CYS E 214 " distance=2.04 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 237 " distance=2.07 Simple disulfide: pdb=" SG CYS E 339 " - pdb=" SG CYS E 349 " distance=2.07 Simple disulfide: pdb=" SG CYS E 383 " - pdb=" SG CYS E 407 " distance=2.86 Simple disulfide: pdb=" SG CYS E 425 " - pdb=" SG CYS E 478 " distance=2.00 Simple disulfide: pdb=" SG CYS E 437 " - pdb=" SG CYS E 585 " distance=2.11 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 526 " distance=2.02 Simple disulfide: pdb=" SG CYS E 603 " - pdb=" SG CYS E 654 " distance=1.76 Simple disulfide: pdb=" SG CYS E 620 " - pdb=" SG CYS E 650 " distance=1.71 Simple disulfide: pdb=" SG CYS E 679 " - pdb=" SG CYS E 713 " distance=2.03 Simple disulfide: pdb=" SG CYS E 727 " - pdb=" SG CYS E 736 " distance=2.02 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 195 " distance=2.06 Simple disulfide: pdb=" SG CYS F 176 " - pdb=" SG CYS F 214 " distance=2.09 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 237 " distance=2.04 Simple disulfide: pdb=" SG CYS F 339 " - pdb=" SG CYS F 349 " distance=2.04 Simple disulfide: pdb=" SG CYS F 383 " - pdb=" SG CYS F 407 " distance=2.17 Simple disulfide: pdb=" SG CYS F 425 " - pdb=" SG CYS F 478 " distance=2.04 Simple disulfide: pdb=" SG CYS F 437 " - pdb=" SG CYS F 585 " distance=2.14 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 526 " distance=2.02 Simple disulfide: pdb=" SG CYS F 603 " - pdb=" SG CYS F 654 " distance=2.10 Simple disulfide: pdb=" SG CYS F 620 " - pdb=" SG CYS F 650 " distance=2.05 Simple disulfide: pdb=" SG CYS F 679 " - pdb=" SG CYS F 713 " distance=2.03 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 736 " distance=2.02 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.05 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.08 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.07 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.04 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=2.07 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.38 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=2.09 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.02 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.23 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.13 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.07 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=1.78 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: 12.07 Conformation dependent library (CDL) restraints added in 5.9 seconds 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7470 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 69 sheets defined 23.6% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.688A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.559A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.506A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.810A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 814 through 821 Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.536A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 922 through 931 removed outlier: 5.390A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL D 929 " --> pdb=" O CYS D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 982 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1011 Processing helix chain 'D' and resid 1016 through 1041 removed outlier: 3.528A pdb=" N LEU D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER D1041 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1058 Processing helix chain 'D' and resid 1059 through 1104 Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'G' and resid 814 through 821 Processing helix chain 'G' and resid 824 through 854 Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.525A pdb=" N ALA G 926 " --> pdb=" O ASP G 922 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN G 927 " --> pdb=" O LEU G 923 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL G 929 " --> pdb=" O CYS G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1011 Processing helix chain 'G' and resid 1016 through 1040 Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1104 removed outlier: 4.326A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.702A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.516A pdb=" N SER E 390 " --> pdb=" O PRO E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 399 removed outlier: 3.716A pdb=" N PHE E 399 " --> pdb=" O VAL E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 415 Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 429 through 436 removed outlier: 3.961A pdb=" N ALA E 434 " --> pdb=" O PRO E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 456 removed outlier: 4.957A pdb=" N SER E 454 " --> pdb=" O SER E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'E' and resid 546 through 550 Processing helix chain 'E' and resid 675 through 678 removed outlier: 3.680A pdb=" N ALA E 678 " --> pdb=" O GLY E 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 675 through 678' Processing helix chain 'E' and resid 694 through 702 removed outlier: 3.615A pdb=" N LYS E 698 " --> pdb=" O ARG E 694 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG E 700 " --> pdb=" O MET E 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 41 removed outlier: 4.156A pdb=" N ASP F 41 " --> pdb=" O THR F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.911A pdb=" N ARG F 307 " --> pdb=" O GLN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 385 through 390 removed outlier: 3.624A pdb=" N SER F 390 " --> pdb=" O PRO F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 399 removed outlier: 4.212A pdb=" N PHE F 399 " --> pdb=" O VAL F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 416 removed outlier: 3.621A pdb=" N LEU F 414 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 449 through 456 removed outlier: 5.168A pdb=" N SER F 454 " --> pdb=" O SER F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 524 through 529 Processing helix chain 'F' and resid 675 through 678 removed outlier: 4.221A pdb=" N ALA F 678 " --> pdb=" O GLY F 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 675 through 678' Processing helix chain 'F' and resid 694 through 702 removed outlier: 4.887A pdb=" N ARG F 700 " --> pdb=" O MET F 696 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 107 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 removed outlier: 3.944A pdb=" N ARG J 307 " --> pdb=" O GLN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 389 Processing helix chain 'J' and resid 410 through 416 removed outlier: 4.072A pdb=" N LEU J 414 " --> pdb=" O ASN J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 436 removed outlier: 3.644A pdb=" N ALA J 434 " --> pdb=" O PRO J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 456 removed outlier: 4.621A pdb=" N SER J 454 " --> pdb=" O SER J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'J' and resid 524 through 529 Processing helix chain 'J' and resid 546 through 550 Processing helix chain 'J' and resid 675 through 678 removed outlier: 4.437A pdb=" N ALA J 678 " --> pdb=" O GLY J 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 675 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 4.837A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 719 through 724 removed outlier: 7.468A pdb=" N LEU A 759 " --> pdb=" O SER E 720 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU E 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.691A pdb=" N ILE A 768 " --> pdb=" O SER D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.908A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 6.178A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.887A pdb=" N ALA B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.418A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 99 removed outlier: 5.485A pdb=" N TYR B 97 " --> pdb=" O ALA B 100D" (cutoff:3.500A) removed outlier: 7.376A pdb=" N ALA B 100D" --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 99 " --> pdb=" O VAL B 100B" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.011A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=AB4, first strand: chain 'F' and resid 719 through 724 removed outlier: 7.116A pdb=" N LEU D 759 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU F 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.754A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 777 through 782 removed outlier: 5.734A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 785 through 796 Processing sheet with id=AB8, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB9, first strand: chain 'D' and resid 1202 through 1204 removed outlier: 6.543A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.222A pdb=" N LEU G 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU J 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY J 732 " --> pdb=" O LEU J 735 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA J 737 " --> pdb=" O PRO J 730 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 777 through 782 removed outlier: 5.917A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 785 through 796 removed outlier: 3.763A pdb=" N VAL G1139 " --> pdb=" O VAL G1124 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AC5, first strand: chain 'G' and resid 1165 through 1167 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.372A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 96 through 99 removed outlier: 5.306A pdb=" N TYR H 97 " --> pdb=" O ALA H 100D" (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA H 100D" --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL H 99 " --> pdb=" O VAL H 100B" (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.757A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 17 through 24 removed outlier: 5.706A pdb=" N GLN I 17 " --> pdb=" O PRO I 77 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.118A pdb=" N ASP E 34 " --> pdb=" O VAL E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 68 through 76 removed outlier: 6.514A pdb=" N SER E 267 " --> pdb=" O GLN E 280 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLN E 280 " --> pdb=" O SER E 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.626A pdb=" N ARG E 335 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 88 through 89 removed outlier: 7.646A pdb=" N SER E 88 " --> pdb=" O ILE E 300 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AD7, first strand: chain 'E' and resid 110 through 111 removed outlier: 4.516A pdb=" N ALA E 146 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU E 180 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR E 241 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA E 182 " --> pdb=" O PHE E 239 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 239 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR E 184 " --> pdb=" O CYS E 237 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N CYS E 237 " --> pdb=" O TYR E 184 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 126 through 127 removed outlier: 4.124A pdb=" N SER E 126 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 309 " --> pdb=" O THR E 139 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AE1, first strand: chain 'E' and resid 359 through 366 removed outlier: 4.114A pdb=" N VAL E 659 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER E 365 " --> pdb=" O VAL E 657 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL E 657 " --> pdb=" O SER E 365 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 374 through 376 Processing sheet with id=AE3, first strand: chain 'E' and resid 400 through 404 removed outlier: 6.649A pdb=" N THR E 483 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL E 420 " --> pdb=" O THR E 483 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 513 through 515 removed outlier: 5.410A pdb=" N SER E 498 " --> pdb=" O VAL E 561 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL E 561 " --> pdb=" O SER E 498 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE E 500 " --> pdb=" O SER E 559 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER E 559 " --> pdb=" O ILE E 500 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 617 through 619 removed outlier: 4.840A pdb=" N VAL E 639 " --> pdb=" O LEU E 651 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 631 " --> pdb=" O VAL E 639 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 33 through 35 removed outlier: 5.903A pdb=" N ASP F 34 " --> pdb=" O VAL F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'F' and resid 69 through 76 removed outlier: 6.475A pdb=" N SER F 267 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLN F 280 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 83 through 85 removed outlier: 3.669A pdb=" N ARG F 335 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 88 through 89 removed outlier: 7.571A pdb=" N SER F 88 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AF2, first strand: chain 'F' and resid 110 through 111 removed outlier: 4.476A pdb=" N ALA F 146 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE F 186 " --> pdb=" O CYS F 237 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N CYS F 237 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU F 188 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG F 235 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.390A pdb=" N SER F 126 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA F 309 " --> pdb=" O THR F 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AF5, first strand: chain 'F' and resid 359 through 366 removed outlier: 3.997A pdb=" N VAL F 659 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER F 365 " --> pdb=" O VAL F 657 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL F 657 " --> pdb=" O SER F 365 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 374 through 375 Processing sheet with id=AF7, first strand: chain 'F' and resid 381 through 382 removed outlier: 6.373A pdb=" N VAL F 381 " --> pdb=" O ASN F 408 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N CYS F 407 " --> pdb=" O CYS F 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'F' and resid 400 through 404 removed outlier: 3.692A pdb=" N LYS F 400 " --> pdb=" O TYR F 445 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR F 483 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL F 420 " --> pdb=" O THR F 483 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 513 through 515 removed outlier: 5.363A pdb=" N SER F 498 " --> pdb=" O VAL F 561 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL F 561 " --> pdb=" O SER F 498 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE F 500 " --> pdb=" O SER F 559 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER F 559 " --> pdb=" O ILE F 500 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 617 through 618 removed outlier: 5.353A pdb=" N VAL F 639 " --> pdb=" O LEU F 651 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL F 631 " --> pdb=" O VAL F 639 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AG3, first strand: chain 'J' and resid 68 through 76 removed outlier: 6.475A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.696A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.607A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AG7, first strand: chain 'J' and resid 109 through 111 removed outlier: 4.437A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU J 180 " --> pdb=" O THR J 242 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR J 242 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA J 182 " --> pdb=" O MET J 240 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET J 240 " --> pdb=" O ALA J 182 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR J 184 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE J 186 " --> pdb=" O ASN J 236 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN J 236 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU J 188 " --> pdb=" O LEU J 234 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU J 234 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.100A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AH1, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.282A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 371 through 375 removed outlier: 7.349A pdb=" N SER J 371 " --> pdb=" O GLU J 605 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N SER J 607 " --> pdb=" O SER J 371 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N SER J 373 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 381 through 382 removed outlier: 6.329A pdb=" N VAL J 381 " --> pdb=" O ASN J 408 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N CYS J 407 " --> pdb=" O CYS J 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'J' and resid 400 through 404 removed outlier: 7.007A pdb=" N THR J 477 " --> pdb=" O CYS J 425 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N CYS J 425 " --> pdb=" O THR J 477 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU J 479 " --> pdb=" O PHE J 423 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE J 423 " --> pdb=" O LEU J 479 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU J 481 " --> pdb=" O ASN J 421 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.454A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 617 through 619 removed outlier: 5.487A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3027 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: 13.94 Time building geometry restraints manager: 13.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6819 1.32 - 1.46: 10617 1.46 - 1.60: 14192 1.60 - 1.73: 1 1.73 - 1.87: 232 Bond restraints: 31861 Sorted by residual: bond pdb=" C CYS J 185 " pdb=" O CYS J 185 " ideal model delta sigma weight residual 1.233 1.301 -0.067 1.17e-02 7.31e+03 3.32e+01 bond pdb=" CA LYS A 807 " pdb=" C LYS A 807 " ideal model delta sigma weight residual 1.521 1.468 0.053 9.90e-03 1.02e+04 2.86e+01 bond pdb=" CA PRO G1219 " pdb=" C PRO G1219 " ideal model delta sigma weight residual 1.517 1.567 -0.050 9.30e-03 1.16e+04 2.85e+01 bond pdb=" N CYS J 185 " pdb=" CA CYS J 185 " ideal model delta sigma weight residual 1.456 1.395 0.061 1.16e-02 7.43e+03 2.79e+01 bond pdb=" C ASN J 236 " pdb=" N CYS J 237 " ideal model delta sigma weight residual 1.331 1.403 -0.072 1.37e-02 5.33e+03 2.76e+01 ... (remaining 31856 not shown) Histogram of bond angle deviations from ideal: 95.49 - 103.56: 252 103.56 - 111.63: 13448 111.63 - 119.70: 14461 119.70 - 127.77: 14975 127.77 - 135.84: 200 Bond angle restraints: 43336 Sorted by residual: angle pdb=" N PRO G1220 " pdb=" CA PRO G1220 " pdb=" C PRO G1220 " ideal model delta sigma weight residual 110.70 125.11 -14.41 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N PRO G1219 " pdb=" CA PRO G1219 " pdb=" C PRO G1219 " ideal model delta sigma weight residual 110.70 124.99 -14.29 1.22e+00 6.72e-01 1.37e+02 angle pdb=" C GLN I 42 " pdb=" N PRO I 43 " pdb=" CA PRO I 43 " ideal model delta sigma weight residual 119.66 127.44 -7.78 7.20e-01 1.93e+00 1.17e+02 angle pdb=" C GLN C 42 " pdb=" N PRO C 43 " pdb=" CA PRO C 43 " ideal model delta sigma weight residual 119.66 127.54 -7.88 7.30e-01 1.88e+00 1.17e+02 angle pdb=" C LEU A 935 " pdb=" N PRO A 936 " pdb=" CA PRO A 936 " ideal model delta sigma weight residual 119.66 126.83 -7.17 7.20e-01 1.93e+00 9.93e+01 ... (remaining 43331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18336 17.98 - 35.97: 448 35.97 - 53.95: 156 53.95 - 71.93: 65 71.93 - 89.92: 21 Dihedral angle restraints: 19026 sinusoidal: 7317 harmonic: 11709 Sorted by residual: dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 166.83 -73.83 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 163.88 -70.88 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS D1106 " pdb=" SG CYS D1106 " pdb=" SG CYS D1117 " pdb=" CB CYS D1117 " ideal model delta sinusoidal sigma weight residual 93.00 158.22 -65.22 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 19023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2962 0.073 - 0.146: 1470 0.146 - 0.219: 325 0.219 - 0.292: 50 0.292 - 0.366: 9 Chirality restraints: 4816 Sorted by residual: chirality pdb=" CA CYS J 727 " pdb=" N CYS J 727 " pdb=" C CYS J 727 " pdb=" CB CYS J 727 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA GLN J 688 " pdb=" N GLN J 688 " pdb=" C GLN J 688 " pdb=" CB GLN J 688 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA LEU F 717 " pdb=" N LEU F 717 " pdb=" C LEU F 717 " pdb=" CB LEU F 717 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 4813 not shown) Planarity restraints: 5634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.089 2.00e-02 2.50e+03 4.51e-02 5.09e+01 pdb=" CG TRP H 47 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 932 " -0.081 2.00e-02 2.50e+03 4.59e-02 4.22e+01 pdb=" CG TYR G 932 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR G 932 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR G 932 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR G 932 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR G 932 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR G 932 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 932 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 603 " -0.029 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C CYS F 603 " 0.102 2.00e-02 2.50e+03 pdb=" O CYS F 603 " -0.041 2.00e-02 2.50e+03 pdb=" N VAL F 604 " -0.032 2.00e-02 2.50e+03 ... (remaining 5631 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.02: 16 2.02 - 2.74: 4100 2.74 - 3.46: 43257 3.46 - 4.18: 77162 4.18 - 4.90: 129736 Nonbonded interactions: 254271 Sorted by model distance: nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.306 3.470 nonbonded pdb=" CG2 VAL E 381 " pdb=" ND2 ASN E 408 " model vdw 1.385 3.540 nonbonded pdb=" CG2 VAL E 381 " pdb=" CG ASN E 408 " model vdw 1.444 3.690 nonbonded pdb=" OH TYR G 905 " pdb=" O VAL G 934 " model vdw 1.598 2.440 nonbonded pdb=" CG1 VAL E 381 " pdb=" N ASN E 408 " model vdw 1.617 3.540 ... (remaining 254266 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 753 through 1176 or resid 1183 through 1223)) selection = chain 'D' selection = (chain 'G' and (resid 753 through 1176 or resid 1183 through 1223)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' 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: 1.560 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: 7.930 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 83.790 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.014 0.072 31861 Z= 0.885 Angle : 1.752 14.409 43336 Z= 1.202 Chirality : 0.085 0.366 4816 Planarity : 0.012 0.121 5634 Dihedral : 10.414 89.917 11391 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.36 % Favored : 96.09 % Rotamer: Outliers : 0.09 % Allowed : 0.41 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.13), residues: 3993 helix: -0.34 (0.17), residues: 658 sheet: 0.79 (0.16), residues: 871 loop : 1.91 (0.13), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.010 TRP H 47 HIS 0.010 0.002 HIS C 76 PHE 0.036 0.005 PHE I 98 TYR 0.081 0.007 TYR G 932 ARG 0.007 0.001 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 609 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1104 ASN cc_start: 0.8838 (m-40) cc_final: 0.7938 (t0) REVERT: B 2 VAL cc_start: 0.7807 (t) cc_final: 0.7333 (t) REVERT: B 28 THR cc_start: 0.8504 (m) cc_final: 0.8207 (p) REVERT: B 32 TYR cc_start: 0.7747 (p90) cc_final: 0.6725 (p90) REVERT: B 35 HIS cc_start: 0.9182 (m-70) cc_final: 0.8828 (m-70) REVERT: B 36 TRP cc_start: 0.8516 (m100) cc_final: 0.7199 (m100) REVERT: B 45 LEU cc_start: 0.9315 (mp) cc_final: 0.9050 (mp) REVERT: B 46 GLU cc_start: 0.8318 (pt0) cc_final: 0.7982 (pt0) REVERT: B 56 ASN cc_start: 0.8594 (m-40) cc_final: 0.8066 (t0) REVERT: B 80 MET cc_start: 0.9355 (tmm) cc_final: 0.9086 (tmm) REVERT: B 82 LEU cc_start: 0.8246 (tt) cc_final: 0.7771 (tt) REVERT: C 33 MET cc_start: 0.7907 (tpp) cc_final: 0.7704 (mmm) REVERT: C 36 PHE cc_start: 0.9221 (m-80) cc_final: 0.8934 (m-80) REVERT: C 85 MET cc_start: 0.9298 (mmm) cc_final: 0.8683 (mmm) REVERT: C 89 GLN cc_start: 0.6940 (tm-30) cc_final: 0.6327 (tm-30) REVERT: D 757 MET cc_start: 0.9174 (mmp) cc_final: 0.8968 (mmm) REVERT: D 780 LEU cc_start: 0.9393 (tp) cc_final: 0.9151 (tt) REVERT: D 793 GLU cc_start: 0.8698 (pt0) cc_final: 0.8482 (pm20) REVERT: D 850 PHE cc_start: 0.8293 (m-10) cc_final: 0.8013 (m-10) REVERT: D 943 MET cc_start: 0.8624 (mtp) cc_final: 0.8422 (ttm) REVERT: D 977 PHE cc_start: 0.9060 (m-80) cc_final: 0.8660 (m-10) REVERT: D 1001 PHE cc_start: 0.9251 (t80) cc_final: 0.8374 (t80) REVERT: D 1136 PHE cc_start: 0.8910 (m-80) cc_final: 0.8372 (m-10) REVERT: D 1190 SER cc_start: 0.8257 (t) cc_final: 0.7804 (t) REVERT: G 874 LEU cc_start: 0.9132 (mt) cc_final: 0.8677 (pp) REVERT: G 875 GLU cc_start: 0.9283 (pm20) cc_final: 0.8114 (pp20) REVERT: G 890 ILE cc_start: 0.9470 (mt) cc_final: 0.9155 (tp) REVERT: G 943 MET cc_start: 0.9305 (mtp) cc_final: 0.8881 (mmm) REVERT: G 944 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9206 (mt-10) REVERT: G 1042 ASN cc_start: 0.9292 (t0) cc_final: 0.8940 (t0) REVERT: G 1075 LEU cc_start: 0.9349 (tp) cc_final: 0.8899 (pp) REVERT: G 1084 GLN cc_start: 0.9550 (tp40) cc_final: 0.9153 (tm-30) REVERT: G 1171 TYR cc_start: 0.8858 (m-80) cc_final: 0.8625 (m-10) REVERT: H 2 VAL cc_start: 0.8980 (t) cc_final: 0.8488 (t) REVERT: H 51 PHE cc_start: 0.8567 (t80) cc_final: 0.8275 (t80) REVERT: H 56 ASN cc_start: 0.8406 (m-40) cc_final: 0.7994 (m110) REVERT: H 80 MET cc_start: 0.8942 (ttp) cc_final: 0.8655 (tpp) REVERT: H 101 ASP cc_start: 0.8312 (t0) cc_final: 0.7381 (t0) REVERT: I 27 ASP cc_start: 0.9115 (m-30) cc_final: 0.8654 (t0) REVERT: I 38 GLN cc_start: 0.8934 (tt0) cc_final: 0.8338 (tt0) REVERT: I 75 ILE cc_start: 0.9326 (mt) cc_final: 0.8879 (tt) REVERT: I 78 VAL cc_start: 0.9234 (t) cc_final: 0.8987 (t) REVERT: I 85 MET cc_start: 0.9124 (mpp) cc_final: 0.8740 (mpp) REVERT: E 56 ILE cc_start: 0.9386 (mm) cc_final: 0.9127 (mm) REVERT: E 367 GLU cc_start: 0.8638 (pt0) cc_final: 0.8398 (tm-30) REVERT: E 382 GLU cc_start: 0.6462 (tp30) cc_final: 0.6229 (mt-10) REVERT: E 638 LEU cc_start: 0.9128 (tp) cc_final: 0.8823 (tp) REVERT: E 662 ILE cc_start: 0.9598 (mp) cc_final: 0.9325 (pt) REVERT: F 49 ASP cc_start: 0.7121 (t0) cc_final: 0.6743 (t0) REVERT: F 278 MET cc_start: 0.8550 (mtm) cc_final: 0.8080 (mtm) REVERT: F 284 LEU cc_start: 0.9525 (mt) cc_final: 0.9302 (tp) REVERT: F 343 ASP cc_start: 0.9260 (m-30) cc_final: 0.8432 (p0) REVERT: F 356 VAL cc_start: 0.8448 (t) cc_final: 0.8237 (m) REVERT: F 686 MET cc_start: 0.7442 (mmm) cc_final: 0.5919 (mmm) REVERT: F 700 ARG cc_start: 0.6552 (mtt90) cc_final: 0.6248 (mmm160) REVERT: J 239 PHE cc_start: 0.8749 (m-80) cc_final: 0.8545 (m-80) REVERT: J 240 MET cc_start: 0.8809 (ppp) cc_final: 0.8597 (ppp) REVERT: J 278 MET cc_start: 0.8101 (mmm) cc_final: 0.7707 (mmm) REVERT: J 284 LEU cc_start: 0.9132 (mt) cc_final: 0.8824 (mp) REVERT: J 333 ILE cc_start: 0.9245 (mt) cc_final: 0.8960 (mm) REVERT: J 346 GLN cc_start: 0.9445 (tp40) cc_final: 0.9203 (mm110) REVERT: J 356 VAL cc_start: 0.8579 (t) cc_final: 0.8374 (t) REVERT: J 529 ILE cc_start: 0.6568 (tp) cc_final: 0.5247 (pt) REVERT: J 576 GLN cc_start: 0.8682 (tp40) cc_final: 0.8277 (tt0) REVERT: J 717 LEU cc_start: 0.8994 (mt) cc_final: 0.8568 (tp) outliers start: 3 outliers final: 0 residues processed: 612 average time/residue: 0.4312 time to fit residues: 417.7090 Evaluate side-chains 293 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 335 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 360 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS A1122 HIS A1217 ASN B 58 ASN C 34 ASN C 76 HIS D1104 ASN G 808 GLN G 836 HIS ** G1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1217 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN E 194 HIS E 688 GLN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN F 167 HIS ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 637 ASN J 98 GLN J 167 HIS J 319 GLN J 377 GLN J 406 ASN J 522 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31861 Z= 0.319 Angle : 0.752 14.983 43336 Z= 0.415 Chirality : 0.046 0.241 4816 Planarity : 0.007 0.076 5634 Dihedral : 5.789 31.789 4371 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.58 % Favored : 96.04 % Rotamer: Outliers : 0.09 % Allowed : 1.97 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.50 % Twisted Proline : 0.51 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.13), residues: 3993 helix: 1.13 (0.20), residues: 645 sheet: 0.21 (0.15), residues: 925 loop : 0.84 (0.13), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 553 HIS 0.007 0.002 HIS H 41 PHE 0.040 0.003 PHE A 850 TYR 0.029 0.002 TYR J 469 ARG 0.007 0.001 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 361 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 809 TYR cc_start: 0.9247 (t80) cc_final: 0.8390 (t80) REVERT: A 843 ASP cc_start: 0.8603 (m-30) cc_final: 0.8379 (m-30) REVERT: A 1036 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9219 (mt) REVERT: A 1192 TYR cc_start: 0.8977 (t80) cc_final: 0.8731 (t80) REVERT: B 28 THR cc_start: 0.8483 (m) cc_final: 0.8011 (p) REVERT: B 35 HIS cc_start: 0.9177 (m-70) cc_final: 0.8778 (m-70) REVERT: B 36 TRP cc_start: 0.8240 (m100) cc_final: 0.7267 (m100) REVERT: C 33 MET cc_start: 0.8517 (tpp) cc_final: 0.7933 (mmm) REVERT: C 36 PHE cc_start: 0.9192 (m-80) cc_final: 0.8754 (m-80) REVERT: C 62 PHE cc_start: 0.8690 (m-80) cc_final: 0.8356 (m-80) REVERT: C 85 MET cc_start: 0.8957 (mmm) cc_final: 0.8598 (mmm) REVERT: D 793 GLU cc_start: 0.8647 (pt0) cc_final: 0.8234 (pm20) REVERT: D 943 MET cc_start: 0.8755 (mtp) cc_final: 0.8249 (ttm) REVERT: D 977 PHE cc_start: 0.8875 (m-80) cc_final: 0.7982 (m-10) REVERT: D 990 LEU cc_start: 0.9450 (mt) cc_final: 0.8535 (mt) REVERT: D 1001 PHE cc_start: 0.9304 (t80) cc_final: 0.8994 (t80) REVERT: D 1136 PHE cc_start: 0.9011 (m-80) cc_final: 0.8433 (m-10) REVERT: D 1137 MET cc_start: 0.8669 (mpp) cc_final: 0.8264 (mpp) REVERT: G 757 MET cc_start: 0.8769 (mmt) cc_final: 0.8471 (tpp) REVERT: G 939 MET cc_start: 0.8219 (tpt) cc_final: 0.7953 (tpt) REVERT: G 943 MET cc_start: 0.9519 (mtp) cc_final: 0.8953 (mmm) REVERT: G 1084 GLN cc_start: 0.9483 (tp40) cc_final: 0.9102 (tm-30) REVERT: H 2 VAL cc_start: 0.8370 (t) cc_final: 0.7890 (t) REVERT: H 31 ASP cc_start: 0.8905 (m-30) cc_final: 0.8454 (m-30) REVERT: H 51 PHE cc_start: 0.8744 (t80) cc_final: 0.8264 (t80) REVERT: H 56 ASN cc_start: 0.8602 (m-40) cc_final: 0.8142 (m110) REVERT: H 80 MET cc_start: 0.8937 (ttp) cc_final: 0.8695 (ttp) REVERT: I 27 ASP cc_start: 0.9152 (m-30) cc_final: 0.8917 (t0) REVERT: I 33 MET cc_start: 0.9137 (tpp) cc_final: 0.8833 (tpp) REVERT: I 75 ILE cc_start: 0.9083 (mt) cc_final: 0.8692 (tt) REVERT: I 78 VAL cc_start: 0.9184 (t) cc_final: 0.8928 (t) REVERT: I 85 MET cc_start: 0.9193 (mpp) cc_final: 0.8505 (mpp) REVERT: I 103 LYS cc_start: 0.9428 (tttt) cc_final: 0.9008 (tptp) REVERT: E 287 TYR cc_start: 0.8660 (p90) cc_final: 0.7973 (p90) REVERT: E 638 LEU cc_start: 0.9142 (tp) cc_final: 0.8873 (tp) REVERT: E 662 ILE cc_start: 0.9670 (mp) cc_final: 0.9408 (pt) REVERT: F 49 ASP cc_start: 0.6963 (t0) cc_final: 0.6585 (t0) REVERT: F 324 LEU cc_start: 0.9436 (mt) cc_final: 0.9235 (mt) REVERT: F 343 ASP cc_start: 0.8757 (m-30) cc_final: 0.8430 (p0) REVERT: F 441 LEU cc_start: 0.8537 (tp) cc_final: 0.8046 (mp) REVERT: F 589 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6493 (pm20) REVERT: F 686 MET cc_start: 0.7185 (mmm) cc_final: 0.6926 (mmm) REVERT: F 700 ARG cc_start: 0.6811 (mtt90) cc_final: 0.6431 (mmm160) REVERT: J 239 PHE cc_start: 0.8615 (m-80) cc_final: 0.8196 (m-80) REVERT: J 240 MET cc_start: 0.9024 (ppp) cc_final: 0.8806 (tmm) REVERT: J 278 MET cc_start: 0.8469 (mmm) cc_final: 0.7505 (mmm) REVERT: J 284 LEU cc_start: 0.9058 (mt) cc_final: 0.8615 (mp) REVERT: J 333 ILE cc_start: 0.9291 (mt) cc_final: 0.9052 (mm) REVERT: J 399 PHE cc_start: 0.6298 (m-10) cc_final: 0.5918 (m-10) REVERT: J 401 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7388 (mpt-90) REVERT: J 686 MET cc_start: 0.7284 (mmt) cc_final: 0.6882 (mmt) REVERT: J 717 LEU cc_start: 0.8872 (mt) cc_final: 0.8535 (tp) outliers start: 3 outliers final: 0 residues processed: 362 average time/residue: 0.4336 time to fit residues: 258.3604 Evaluate side-chains 226 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 200 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 chunk 390 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 chunk 358 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 61 GLN D1104 ASN ** D1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN E 475 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 377 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31861 Z= 0.246 Angle : 0.645 12.523 43336 Z= 0.356 Chirality : 0.043 0.234 4816 Planarity : 0.006 0.076 5634 Dihedral : 5.311 33.045 4371 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.48 % Favored : 95.22 % Rotamer: Outliers : 0.06 % Allowed : 1.97 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.13), residues: 3993 helix: 1.24 (0.20), residues: 664 sheet: 0.13 (0.16), residues: 917 loop : 0.61 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 553 HIS 0.005 0.001 HIS E 670 PHE 0.031 0.002 PHE A 850 TYR 0.033 0.002 TYR D1211 ARG 0.007 0.000 ARG J 626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 309 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8450 (tpt) cc_final: 0.8240 (tpt) REVERT: A 1042 ASN cc_start: 0.9027 (t0) cc_final: 0.8822 (t0) REVERT: B 28 THR cc_start: 0.8299 (m) cc_final: 0.7541 (p) REVERT: B 35 HIS cc_start: 0.9158 (m-70) cc_final: 0.8770 (m-70) REVERT: B 56 ASN cc_start: 0.8616 (t0) cc_final: 0.8360 (t0) REVERT: C 36 PHE cc_start: 0.9191 (m-80) cc_final: 0.8802 (m-80) REVERT: C 85 MET cc_start: 0.8989 (mmm) cc_final: 0.8626 (mmm) REVERT: D 835 LEU cc_start: 0.9701 (mm) cc_final: 0.9365 (tp) REVERT: D 943 MET cc_start: 0.8650 (mtp) cc_final: 0.8417 (ttt) REVERT: D 977 PHE cc_start: 0.8880 (m-80) cc_final: 0.8122 (m-10) REVERT: D 990 LEU cc_start: 0.9488 (mt) cc_final: 0.8594 (mt) REVERT: D 1001 PHE cc_start: 0.9311 (t80) cc_final: 0.8959 (t80) REVERT: D 1067 ILE cc_start: 0.9578 (mt) cc_final: 0.9193 (tt) REVERT: D 1136 PHE cc_start: 0.9096 (m-80) cc_final: 0.8712 (m-10) REVERT: G 757 MET cc_start: 0.8851 (mmt) cc_final: 0.8504 (tpp) REVERT: G 932 TYR cc_start: 0.7450 (t80) cc_final: 0.7022 (t80) REVERT: G 939 MET cc_start: 0.8247 (tpt) cc_final: 0.7958 (tpt) REVERT: G 943 MET cc_start: 0.9517 (mtp) cc_final: 0.8968 (mmm) REVERT: G 1042 ASN cc_start: 0.9021 (t0) cc_final: 0.8794 (t0) REVERT: G 1084 GLN cc_start: 0.9523 (tp40) cc_final: 0.9082 (tm-30) REVERT: H 2 VAL cc_start: 0.8392 (t) cc_final: 0.7858 (t) REVERT: H 31 ASP cc_start: 0.8893 (m-30) cc_final: 0.8505 (m-30) REVERT: H 35 HIS cc_start: 0.8124 (m170) cc_final: 0.7859 (m170) REVERT: H 51 PHE cc_start: 0.8711 (t80) cc_final: 0.8147 (t80) REVERT: H 56 ASN cc_start: 0.8699 (m-40) cc_final: 0.8384 (m-40) REVERT: H 101 ASP cc_start: 0.8422 (t0) cc_final: 0.7585 (t0) REVERT: I 33 MET cc_start: 0.9116 (tpp) cc_final: 0.8758 (tpp) REVERT: I 85 MET cc_start: 0.9252 (mpp) cc_final: 0.8301 (mpp) REVERT: I 103 LYS cc_start: 0.9382 (tttt) cc_final: 0.9014 (tptp) REVERT: E 183 PHE cc_start: 0.9121 (m-80) cc_final: 0.8835 (m-80) REVERT: E 287 TYR cc_start: 0.8697 (p90) cc_final: 0.7969 (p90) REVERT: E 638 LEU cc_start: 0.9124 (tp) cc_final: 0.8881 (tp) REVERT: E 662 ILE cc_start: 0.9691 (mp) cc_final: 0.9467 (pt) REVERT: E 704 TYR cc_start: 0.5126 (t80) cc_final: 0.4899 (t80) REVERT: F 49 ASP cc_start: 0.7068 (t0) cc_final: 0.6612 (t0) REVERT: F 256 ILE cc_start: 0.8921 (mm) cc_final: 0.8525 (mm) REVERT: F 343 ASP cc_start: 0.8759 (m-30) cc_final: 0.8495 (p0) REVERT: F 441 LEU cc_start: 0.8530 (tp) cc_final: 0.8030 (mp) REVERT: F 479 LEU cc_start: 0.7735 (mt) cc_final: 0.7446 (tp) REVERT: F 589 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6545 (pm20) REVERT: F 686 MET cc_start: 0.7109 (mmm) cc_final: 0.6310 (mmm) REVERT: J 241 TYR cc_start: 0.8573 (m-80) cc_final: 0.8268 (m-80) REVERT: J 278 MET cc_start: 0.8471 (mmm) cc_final: 0.7466 (mmm) REVERT: J 284 LEU cc_start: 0.9000 (mt) cc_final: 0.8628 (mp) REVERT: J 333 ILE cc_start: 0.9358 (mt) cc_final: 0.9123 (mm) REVERT: J 401 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7503 (mpt-90) REVERT: J 686 MET cc_start: 0.7511 (mmt) cc_final: 0.6609 (mmm) REVERT: J 717 LEU cc_start: 0.8949 (mt) cc_final: 0.8643 (tp) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 0.4013 time to fit residues: 205.8588 Evaluate side-chains 223 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 356 optimal weight: 10.0000 chunk 271 optimal weight: 30.0000 chunk 187 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 362 optimal weight: 1.9990 chunk 383 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 343 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN D 815 GLN ** D1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1084 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN E 466 GLN ** E 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN F 406 ASN ** J 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31861 Z= 0.341 Angle : 0.727 11.545 43336 Z= 0.393 Chirality : 0.045 0.280 4816 Planarity : 0.006 0.059 5634 Dihedral : 5.524 33.257 4371 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.18 % Favored : 94.52 % Rotamer: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 3993 helix: 0.63 (0.19), residues: 699 sheet: -0.20 (0.16), residues: 970 loop : 0.14 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 553 HIS 0.009 0.002 HIS E 670 PHE 0.027 0.002 PHE C 62 TYR 0.031 0.002 TYR J 609 ARG 0.009 0.001 ARG J 626 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8499 (tpt) cc_final: 0.8216 (tpt) REVERT: A 1042 ASN cc_start: 0.8970 (t0) cc_final: 0.8719 (t0) REVERT: A 1084 GLN cc_start: 0.9428 (tp-100) cc_final: 0.8970 (tm-30) REVERT: B 28 THR cc_start: 0.8458 (m) cc_final: 0.8051 (p) REVERT: B 56 ASN cc_start: 0.8633 (t0) cc_final: 0.8350 (t0) REVERT: B 80 MET cc_start: 0.9070 (ttm) cc_final: 0.8520 (ttp) REVERT: C 36 PHE cc_start: 0.9178 (m-80) cc_final: 0.8839 (m-80) REVERT: C 62 PHE cc_start: 0.8817 (m-80) cc_final: 0.8573 (m-80) REVERT: C 85 MET cc_start: 0.8956 (mmm) cc_final: 0.8643 (mmm) REVERT: D 1001 PHE cc_start: 0.9357 (t80) cc_final: 0.9006 (t80) REVERT: D 1067 ILE cc_start: 0.9614 (mt) cc_final: 0.9235 (tt) REVERT: G 757 MET cc_start: 0.8988 (mmt) cc_final: 0.8512 (tpp) REVERT: G 939 MET cc_start: 0.8397 (tpt) cc_final: 0.7597 (tpp) REVERT: G 943 MET cc_start: 0.9511 (mtp) cc_final: 0.8784 (mmm) REVERT: G 1039 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9014 (tp30) REVERT: G 1042 ASN cc_start: 0.9094 (t0) cc_final: 0.8468 (t0) REVERT: G 1084 GLN cc_start: 0.9522 (tp-100) cc_final: 0.9092 (tm-30) REVERT: H 31 ASP cc_start: 0.8933 (m-30) cc_final: 0.8492 (m-30) REVERT: H 51 PHE cc_start: 0.8420 (t80) cc_final: 0.7925 (t80) REVERT: H 56 ASN cc_start: 0.8697 (m-40) cc_final: 0.8260 (m110) REVERT: H 80 MET cc_start: 0.9062 (ttp) cc_final: 0.8511 (tpp) REVERT: I 32 PHE cc_start: 0.9084 (m-10) cc_final: 0.8802 (m-10) REVERT: I 33 MET cc_start: 0.9105 (tpp) cc_final: 0.8709 (tpp) REVERT: I 46 LEU cc_start: 0.9302 (tt) cc_final: 0.8989 (tp) REVERT: I 85 MET cc_start: 0.9158 (mpp) cc_final: 0.7895 (mpp) REVERT: I 103 LYS cc_start: 0.9422 (tttt) cc_final: 0.9068 (tptp) REVERT: E 287 TYR cc_start: 0.8669 (p90) cc_final: 0.7928 (p90) REVERT: E 452 MET cc_start: 0.2961 (ttt) cc_final: 0.2733 (ttt) REVERT: E 638 LEU cc_start: 0.9301 (tp) cc_final: 0.9080 (tp) REVERT: E 704 TYR cc_start: 0.5119 (t80) cc_final: 0.4839 (t80) REVERT: F 49 ASP cc_start: 0.7088 (t0) cc_final: 0.6531 (t0) REVERT: F 343 ASP cc_start: 0.8778 (m-30) cc_final: 0.8533 (p0) REVERT: F 479 LEU cc_start: 0.7695 (mt) cc_final: 0.7431 (tp) REVERT: F 589 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6565 (pm20) REVERT: F 686 MET cc_start: 0.7567 (mmm) cc_final: 0.7358 (mmm) REVERT: F 700 ARG cc_start: 0.7037 (mtt90) cc_final: 0.6649 (mmm160) REVERT: F 725 GLU cc_start: 0.8874 (pm20) cc_final: 0.7650 (tp30) REVERT: J 148 MET cc_start: 0.9387 (ttm) cc_final: 0.9005 (tpp) REVERT: J 278 MET cc_start: 0.8432 (mmm) cc_final: 0.7657 (mmm) REVERT: J 284 LEU cc_start: 0.8952 (mt) cc_final: 0.8669 (mt) REVERT: J 333 ILE cc_start: 0.9401 (mt) cc_final: 0.9156 (mm) REVERT: J 401 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7522 (mpt-90) REVERT: J 563 MET cc_start: 0.6945 (mmm) cc_final: 0.6587 (tpt) REVERT: J 569 MET cc_start: 0.4134 (ptm) cc_final: 0.3513 (ppp) REVERT: J 576 GLN cc_start: 0.8216 (tp40) cc_final: 0.7643 (tt0) REVERT: J 686 MET cc_start: 0.7715 (mmt) cc_final: 0.7351 (mmm) REVERT: J 696 MET cc_start: 0.6077 (mmm) cc_final: 0.5867 (mmm) REVERT: J 700 ARG cc_start: 0.4577 (mmt180) cc_final: 0.3743 (mmm160) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.4052 time to fit residues: 186.6790 Evaluate side-chains 193 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 319 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 285 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 327 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 195 optimal weight: 40.0000 chunk 344 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 993 ASN ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN D 839 ASN ** D1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1212 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 421 ASN F 406 ASN J 280 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31861 Z= 0.291 Angle : 0.656 9.250 43336 Z= 0.357 Chirality : 0.043 0.188 4816 Planarity : 0.005 0.058 5634 Dihedral : 5.443 34.413 4371 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.74 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.13), residues: 3993 helix: 0.69 (0.19), residues: 711 sheet: -0.27 (0.16), residues: 971 loop : -0.02 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 253 HIS 0.006 0.001 HIS E 670 PHE 0.025 0.002 PHE A 850 TYR 0.020 0.002 TYR A 978 ARG 0.006 0.001 ARG J 626 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8399 (tpt) cc_final: 0.8170 (tpt) REVERT: A 943 MET cc_start: 0.9114 (tpp) cc_final: 0.8880 (tpt) REVERT: A 1042 ASN cc_start: 0.8675 (t0) cc_final: 0.8370 (t0) REVERT: A 1084 GLN cc_start: 0.9394 (tp-100) cc_final: 0.9092 (tm-30) REVERT: B 2 VAL cc_start: 0.7675 (t) cc_final: 0.7447 (t) REVERT: B 28 THR cc_start: 0.8341 (m) cc_final: 0.7977 (p) REVERT: B 56 ASN cc_start: 0.8594 (t0) cc_final: 0.8335 (t0) REVERT: C 33 MET cc_start: 0.8136 (tpt) cc_final: 0.7576 (mmm) REVERT: C 36 PHE cc_start: 0.9160 (m-80) cc_final: 0.8843 (m-80) REVERT: C 62 PHE cc_start: 0.8759 (m-80) cc_final: 0.8478 (m-80) REVERT: C 85 MET cc_start: 0.8962 (mmm) cc_final: 0.8585 (mmm) REVERT: D 977 PHE cc_start: 0.8919 (m-80) cc_final: 0.8335 (m-80) REVERT: D 1001 PHE cc_start: 0.9339 (t80) cc_final: 0.9030 (t80) REVERT: D 1067 ILE cc_start: 0.9602 (mt) cc_final: 0.9210 (tt) REVERT: G 757 MET cc_start: 0.9006 (mmt) cc_final: 0.8736 (mmt) REVERT: G 843 ASP cc_start: 0.9432 (p0) cc_final: 0.9227 (p0) REVERT: G 939 MET cc_start: 0.8447 (tpt) cc_final: 0.7811 (tpp) REVERT: G 943 MET cc_start: 0.9472 (mtp) cc_final: 0.8755 (mmm) REVERT: G 1042 ASN cc_start: 0.9095 (t0) cc_final: 0.8788 (t0) REVERT: G 1084 GLN cc_start: 0.9515 (tp-100) cc_final: 0.9052 (tm-30) REVERT: H 2 VAL cc_start: 0.8703 (t) cc_final: 0.8069 (t) REVERT: H 31 ASP cc_start: 0.8940 (m-30) cc_final: 0.8423 (m-30) REVERT: H 51 PHE cc_start: 0.8297 (t80) cc_final: 0.7764 (t80) REVERT: H 56 ASN cc_start: 0.8737 (m-40) cc_final: 0.8368 (m110) REVERT: I 32 PHE cc_start: 0.9015 (m-10) cc_final: 0.8652 (m-10) REVERT: I 33 MET cc_start: 0.9157 (tpp) cc_final: 0.8831 (tpp) REVERT: I 85 MET cc_start: 0.9145 (mpp) cc_final: 0.8331 (mpp) REVERT: I 103 LYS cc_start: 0.9424 (tttt) cc_final: 0.9164 (tttp) REVERT: E 452 MET cc_start: 0.2744 (ttt) cc_final: 0.2534 (ttt) REVERT: E 638 LEU cc_start: 0.9309 (tp) cc_final: 0.9107 (tp) REVERT: E 704 TYR cc_start: 0.5096 (t80) cc_final: 0.4795 (t80) REVERT: F 49 ASP cc_start: 0.7060 (t0) cc_final: 0.6525 (t0) REVERT: F 343 ASP cc_start: 0.8757 (m-30) cc_final: 0.8512 (p0) REVERT: F 479 LEU cc_start: 0.7753 (mt) cc_final: 0.7467 (tp) REVERT: F 589 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6584 (pm20) REVERT: F 686 MET cc_start: 0.7723 (mmm) cc_final: 0.7507 (mmm) REVERT: F 700 ARG cc_start: 0.7039 (mtt90) cc_final: 0.6707 (mmm160) REVERT: F 725 GLU cc_start: 0.8831 (pm20) cc_final: 0.7615 (tp30) REVERT: J 148 MET cc_start: 0.9402 (ttm) cc_final: 0.9057 (tpp) REVERT: J 278 MET cc_start: 0.8386 (mmm) cc_final: 0.7892 (mmm) REVERT: J 333 ILE cc_start: 0.9396 (mt) cc_final: 0.9159 (mm) REVERT: J 523 TYR cc_start: 0.6631 (m-10) cc_final: 0.6093 (m-80) REVERT: J 563 MET cc_start: 0.6928 (mmm) cc_final: 0.6653 (tpp) REVERT: J 700 ARG cc_start: 0.4653 (mmt180) cc_final: 0.3979 (mmm160) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.4095 time to fit residues: 177.2490 Evaluate side-chains 193 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 129 optimal weight: 0.9980 chunk 345 optimal weight: 20.0000 chunk 75 optimal weight: 0.0040 chunk 225 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 384 optimal weight: 7.9990 chunk 318 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 overall best weight: 2.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1028 ASN G1031 GLN I 37 GLN F 167 HIS ** F 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 ASN J 348 HIS J 733 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31861 Z= 0.189 Angle : 0.587 9.754 43336 Z= 0.317 Chirality : 0.042 0.192 4816 Planarity : 0.005 0.052 5634 Dihedral : 5.124 31.973 4371 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.06 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 3993 helix: 1.01 (0.20), residues: 717 sheet: -0.04 (0.16), residues: 945 loop : -0.07 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 553 HIS 0.008 0.001 HIS J 348 PHE 0.023 0.001 PHE A 850 TYR 0.018 0.001 TYR C 28 ARG 0.006 0.000 ARG J 626 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8360 (tpt) cc_final: 0.8108 (tpt) REVERT: A 943 MET cc_start: 0.9060 (tpp) cc_final: 0.8856 (tpt) REVERT: A 1005 LEU cc_start: 0.9385 (mt) cc_final: 0.9171 (mt) REVERT: A 1036 LEU cc_start: 0.9663 (tp) cc_final: 0.9418 (tp) REVERT: A 1039 GLU cc_start: 0.8536 (mp0) cc_final: 0.8331 (mp0) REVERT: A 1042 ASN cc_start: 0.8697 (t0) cc_final: 0.8411 (t0) REVERT: A 1084 GLN cc_start: 0.9356 (tp-100) cc_final: 0.9067 (tm-30) REVERT: B 3 GLN cc_start: 0.8653 (pt0) cc_final: 0.8372 (pm20) REVERT: B 28 THR cc_start: 0.8280 (m) cc_final: 0.7911 (p) REVERT: B 35 HIS cc_start: 0.9208 (m-70) cc_final: 0.8915 (m-70) REVERT: B 36 TRP cc_start: 0.8659 (m100) cc_final: 0.6872 (m100) REVERT: B 56 ASN cc_start: 0.8645 (t0) cc_final: 0.8376 (t0) REVERT: B 80 MET cc_start: 0.8522 (ttm) cc_final: 0.8145 (tmm) REVERT: C 33 MET cc_start: 0.8145 (tpt) cc_final: 0.7743 (mmm) REVERT: C 36 PHE cc_start: 0.9188 (m-80) cc_final: 0.8855 (m-80) REVERT: C 85 MET cc_start: 0.8958 (mmm) cc_final: 0.8557 (mmm) REVERT: D 771 ASP cc_start: 0.8977 (m-30) cc_final: 0.8667 (t0) REVERT: D 839 ASN cc_start: 0.9317 (m-40) cc_final: 0.8620 (m-40) REVERT: D 943 MET cc_start: 0.9065 (mmm) cc_final: 0.8755 (tpt) REVERT: D 977 PHE cc_start: 0.8920 (m-80) cc_final: 0.8458 (m-10) REVERT: D 1001 PHE cc_start: 0.9313 (t80) cc_final: 0.8891 (t80) REVERT: D 1067 ILE cc_start: 0.9584 (mt) cc_final: 0.9185 (tt) REVERT: G 757 MET cc_start: 0.8999 (mmt) cc_final: 0.8771 (mmt) REVERT: G 933 LYS cc_start: 0.9027 (tppt) cc_final: 0.8730 (tptt) REVERT: G 939 MET cc_start: 0.8380 (tpt) cc_final: 0.7849 (tpp) REVERT: G 943 MET cc_start: 0.9412 (mtp) cc_final: 0.8677 (mmm) REVERT: G 1042 ASN cc_start: 0.9170 (t0) cc_final: 0.8188 (t0) REVERT: G 1084 GLN cc_start: 0.9457 (tp-100) cc_final: 0.8995 (tm-30) REVERT: H 2 VAL cc_start: 0.8693 (t) cc_final: 0.8111 (t) REVERT: H 31 ASP cc_start: 0.8919 (m-30) cc_final: 0.8410 (m-30) REVERT: H 51 PHE cc_start: 0.8270 (t80) cc_final: 0.7774 (t80) REVERT: H 56 ASN cc_start: 0.8746 (m-40) cc_final: 0.8398 (m110) REVERT: I 32 PHE cc_start: 0.9021 (m-10) cc_final: 0.8474 (m-10) REVERT: I 33 MET cc_start: 0.9156 (tpp) cc_final: 0.8823 (tpp) REVERT: I 73 LEU cc_start: 0.9412 (tt) cc_final: 0.9179 (tt) REVERT: I 85 MET cc_start: 0.9124 (mpp) cc_final: 0.8389 (mpp) REVERT: I 103 LYS cc_start: 0.9368 (tttt) cc_final: 0.9088 (tttp) REVERT: E 452 MET cc_start: 0.2526 (ttt) cc_final: 0.2252 (ttt) REVERT: E 638 LEU cc_start: 0.9309 (tp) cc_final: 0.9048 (tp) REVERT: E 704 TYR cc_start: 0.5112 (t80) cc_final: 0.4804 (t80) REVERT: F 49 ASP cc_start: 0.7137 (t0) cc_final: 0.6694 (t0) REVERT: F 278 MET cc_start: 0.8838 (mmm) cc_final: 0.8470 (mmt) REVERT: F 324 LEU cc_start: 0.9508 (mt) cc_final: 0.9307 (mt) REVERT: F 343 ASP cc_start: 0.8781 (m-30) cc_final: 0.8497 (p0) REVERT: F 589 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6600 (pm20) REVERT: F 686 MET cc_start: 0.7728 (mmm) cc_final: 0.7523 (mmm) REVERT: F 700 ARG cc_start: 0.7027 (mtt90) cc_final: 0.6488 (mmm160) REVERT: F 725 GLU cc_start: 0.8850 (pm20) cc_final: 0.7706 (tp30) REVERT: J 148 MET cc_start: 0.9439 (ttm) cc_final: 0.9088 (tpp) REVERT: J 278 MET cc_start: 0.8313 (mmm) cc_final: 0.7757 (mmm) REVERT: J 333 ILE cc_start: 0.9417 (mt) cc_final: 0.9184 (mm) REVERT: J 523 TYR cc_start: 0.6975 (m-10) cc_final: 0.6414 (m-80) REVERT: J 563 MET cc_start: 0.6929 (mmm) cc_final: 0.6611 (tpp) REVERT: J 686 MET cc_start: 0.7133 (mmm) cc_final: 0.6511 (mmm) REVERT: J 696 MET cc_start: 0.6025 (mmm) cc_final: 0.5726 (mmm) REVERT: J 700 ARG cc_start: 0.4693 (mmt180) cc_final: 0.3903 (mmm160) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.4114 time to fit residues: 184.6345 Evaluate side-chains 199 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 370 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 chunk 217 optimal weight: 20.0000 chunk 323 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 382 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 233 optimal weight: 50.0000 chunk 176 optimal weight: 5.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1145 ASN D1208 GLN ** G 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 987 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 ASN J 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31861 Z= 0.317 Angle : 0.669 9.256 43336 Z= 0.362 Chirality : 0.043 0.181 4816 Planarity : 0.005 0.057 5634 Dihedral : 5.396 34.098 4371 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.49 % Favored : 93.24 % Rotamer: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 3993 helix: 0.68 (0.19), residues: 731 sheet: -0.22 (0.16), residues: 947 loop : -0.35 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 553 HIS 0.008 0.002 HIS E 670 PHE 0.032 0.002 PHE D 850 TYR 0.021 0.002 TYR J 351 ARG 0.009 0.001 ARG D1057 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8413 (tpt) cc_final: 0.8191 (tpt) REVERT: A 1005 LEU cc_start: 0.9461 (mt) cc_final: 0.9211 (mt) REVERT: A 1042 ASN cc_start: 0.8813 (t0) cc_final: 0.8486 (t0) REVERT: A 1084 GLN cc_start: 0.9400 (tp-100) cc_final: 0.9065 (tm-30) REVERT: B 28 THR cc_start: 0.8324 (m) cc_final: 0.7925 (p) REVERT: B 56 ASN cc_start: 0.8540 (t0) cc_final: 0.8303 (t0) REVERT: B 80 MET cc_start: 0.8779 (ttm) cc_final: 0.8274 (tmm) REVERT: C 33 MET cc_start: 0.8075 (tpt) cc_final: 0.7509 (mmm) REVERT: C 36 PHE cc_start: 0.9182 (m-80) cc_final: 0.8877 (m-80) REVERT: C 62 PHE cc_start: 0.8725 (m-80) cc_final: 0.8349 (m-80) REVERT: C 85 MET cc_start: 0.8976 (mmm) cc_final: 0.8565 (mmm) REVERT: D 839 ASN cc_start: 0.9315 (m-40) cc_final: 0.8675 (m-40) REVERT: D 943 MET cc_start: 0.8724 (mmm) cc_final: 0.8401 (tpt) REVERT: D 944 GLU cc_start: 0.8555 (pp20) cc_final: 0.8237 (pp20) REVERT: D 977 PHE cc_start: 0.8866 (m-80) cc_final: 0.8356 (m-10) REVERT: D 1001 PHE cc_start: 0.9384 (t80) cc_final: 0.9006 (t80) REVERT: D 1067 ILE cc_start: 0.9602 (mt) cc_final: 0.9197 (tt) REVERT: G 757 MET cc_start: 0.8967 (mmt) cc_final: 0.8685 (mmt) REVERT: G 939 MET cc_start: 0.8443 (tpt) cc_final: 0.7770 (tpp) REVERT: G 943 MET cc_start: 0.9488 (mtp) cc_final: 0.8734 (mmm) REVERT: G 1084 GLN cc_start: 0.9502 (tp-100) cc_final: 0.9037 (tm-30) REVERT: H 2 VAL cc_start: 0.8805 (t) cc_final: 0.8164 (t) REVERT: H 31 ASP cc_start: 0.8964 (m-30) cc_final: 0.8483 (m-30) REVERT: H 46 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7838 (tm-30) REVERT: H 51 PHE cc_start: 0.8101 (t80) cc_final: 0.7854 (t80) REVERT: I 32 PHE cc_start: 0.8663 (m-10) cc_final: 0.8368 (m-80) REVERT: I 33 MET cc_start: 0.9182 (tpp) cc_final: 0.8831 (tmm) REVERT: I 49 SER cc_start: 0.8478 (m) cc_final: 0.8147 (t) REVERT: I 85 MET cc_start: 0.9158 (mpp) cc_final: 0.8422 (mpp) REVERT: I 103 LYS cc_start: 0.9381 (tttt) cc_final: 0.9108 (tttp) REVERT: E 240 MET cc_start: 0.8352 (mmm) cc_final: 0.8148 (mmm) REVERT: E 452 MET cc_start: 0.2627 (ttt) cc_final: 0.2343 (ttt) REVERT: E 638 LEU cc_start: 0.9279 (tp) cc_final: 0.9064 (tp) REVERT: E 704 TYR cc_start: 0.5018 (t80) cc_final: 0.4497 (t80) REVERT: F 49 ASP cc_start: 0.7093 (t0) cc_final: 0.6655 (t0) REVERT: F 71 TYR cc_start: 0.9072 (t80) cc_final: 0.8795 (t80) REVERT: F 589 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6586 (pm20) REVERT: F 700 ARG cc_start: 0.7123 (mtt90) cc_final: 0.6701 (mmm160) REVERT: F 725 GLU cc_start: 0.8912 (pm20) cc_final: 0.7762 (tp30) REVERT: J 148 MET cc_start: 0.9427 (ttm) cc_final: 0.9113 (tpp) REVERT: J 239 PHE cc_start: 0.8361 (m-80) cc_final: 0.7983 (m-80) REVERT: J 278 MET cc_start: 0.8253 (mmm) cc_final: 0.7991 (mmm) REVERT: J 313 PHE cc_start: 0.7113 (t80) cc_final: 0.6631 (t80) REVERT: J 333 ILE cc_start: 0.9423 (mt) cc_final: 0.9211 (mm) REVERT: J 523 TYR cc_start: 0.7008 (m-10) cc_final: 0.6405 (m-80) REVERT: J 563 MET cc_start: 0.6840 (mmm) cc_final: 0.6590 (tpp) REVERT: J 696 MET cc_start: 0.6093 (mmm) cc_final: 0.5788 (mmm) REVERT: J 700 ARG cc_start: 0.4765 (mmt180) cc_final: 0.3976 (mmm160) REVERT: J 717 LEU cc_start: 0.8960 (mm) cc_final: 0.8753 (mp) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.3997 time to fit residues: 165.8956 Evaluate side-chains 186 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 236 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 228 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 243 optimal weight: 30.0000 chunk 260 optimal weight: 30.0000 chunk 189 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 300 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 HIS A1138 HIS A1212 GLN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1028 ASN ** G1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN F 406 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31861 Z= 0.236 Angle : 0.611 9.699 43336 Z= 0.331 Chirality : 0.043 0.172 4816 Planarity : 0.005 0.054 5634 Dihedral : 5.236 32.074 4371 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 3993 helix: 0.88 (0.19), residues: 725 sheet: -0.26 (0.16), residues: 920 loop : -0.39 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 253 HIS 0.006 0.001 HIS E 670 PHE 0.022 0.002 PHE C 62 TYR 0.018 0.002 TYR D 932 ARG 0.011 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 3.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1042 ASN cc_start: 0.8773 (t0) cc_final: 0.8504 (t0) REVERT: A 1084 GLN cc_start: 0.9353 (tp-100) cc_final: 0.9047 (tm-30) REVERT: B 28 THR cc_start: 0.8285 (m) cc_final: 0.7894 (p) REVERT: B 36 TRP cc_start: 0.8725 (m100) cc_final: 0.6767 (m100) REVERT: B 56 ASN cc_start: 0.8490 (t0) cc_final: 0.8256 (t0) REVERT: B 80 MET cc_start: 0.8794 (ttm) cc_final: 0.8228 (tmm) REVERT: C 62 PHE cc_start: 0.8685 (m-80) cc_final: 0.8351 (m-80) REVERT: C 85 MET cc_start: 0.8984 (mmm) cc_final: 0.8495 (mmm) REVERT: D 839 ASN cc_start: 0.9332 (m-40) cc_final: 0.8733 (m-40) REVERT: D 943 MET cc_start: 0.8739 (mmm) cc_final: 0.8383 (tpt) REVERT: D 977 PHE cc_start: 0.8880 (m-80) cc_final: 0.8439 (m-10) REVERT: D 1001 PHE cc_start: 0.9339 (t80) cc_final: 0.8922 (t80) REVERT: D 1067 ILE cc_start: 0.9598 (mt) cc_final: 0.9169 (tt) REVERT: G 757 MET cc_start: 0.9001 (mmt) cc_final: 0.8705 (mmt) REVERT: G 939 MET cc_start: 0.8519 (tpt) cc_final: 0.7857 (tpp) REVERT: G 943 MET cc_start: 0.9452 (mtp) cc_final: 0.8700 (mmm) REVERT: G 1084 GLN cc_start: 0.9452 (tp-100) cc_final: 0.8991 (tm-30) REVERT: H 2 VAL cc_start: 0.8811 (t) cc_final: 0.8090 (t) REVERT: H 31 ASP cc_start: 0.8908 (m-30) cc_final: 0.8506 (m-30) REVERT: I 32 PHE cc_start: 0.8684 (m-10) cc_final: 0.8187 (m-80) REVERT: I 33 MET cc_start: 0.9177 (tpp) cc_final: 0.8848 (tmm) REVERT: I 49 SER cc_start: 0.8512 (m) cc_final: 0.8219 (t) REVERT: I 73 LEU cc_start: 0.9344 (tt) cc_final: 0.9006 (tp) REVERT: I 85 MET cc_start: 0.9142 (mpp) cc_final: 0.8411 (mpp) REVERT: I 103 LYS cc_start: 0.9373 (tttt) cc_final: 0.9101 (tttp) REVERT: E 240 MET cc_start: 0.8375 (mmm) cc_final: 0.8143 (mmm) REVERT: E 452 MET cc_start: 0.2295 (ttt) cc_final: 0.1997 (ttt) REVERT: E 638 LEU cc_start: 0.9367 (tp) cc_final: 0.9155 (tp) REVERT: E 686 MET cc_start: 0.7459 (tpt) cc_final: 0.6944 (mmm) REVERT: E 704 TYR cc_start: 0.5035 (t80) cc_final: 0.4409 (t80) REVERT: F 49 ASP cc_start: 0.7102 (t0) cc_final: 0.6619 (t0) REVERT: F 71 TYR cc_start: 0.9083 (t80) cc_final: 0.8776 (t80) REVERT: F 278 MET cc_start: 0.8708 (mmp) cc_final: 0.8324 (mmp) REVERT: F 324 LEU cc_start: 0.9481 (mt) cc_final: 0.9267 (mt) REVERT: F 343 ASP cc_start: 0.8821 (m-30) cc_final: 0.8404 (p0) REVERT: F 589 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6594 (pm20) REVERT: F 700 ARG cc_start: 0.7033 (mtt90) cc_final: 0.6638 (mmm160) REVERT: F 725 GLU cc_start: 0.8865 (pm20) cc_final: 0.7725 (tp30) REVERT: J 148 MET cc_start: 0.9441 (ttm) cc_final: 0.9120 (tpp) REVERT: J 239 PHE cc_start: 0.8327 (m-80) cc_final: 0.7961 (m-80) REVERT: J 278 MET cc_start: 0.8176 (mmm) cc_final: 0.7912 (mmm) REVERT: J 523 TYR cc_start: 0.6973 (m-10) cc_final: 0.6319 (m-80) REVERT: J 696 MET cc_start: 0.5925 (mmm) cc_final: 0.5619 (mmm) REVERT: J 700 ARG cc_start: 0.4659 (mmt180) cc_final: 0.3915 (mmm160) REVERT: J 717 LEU cc_start: 0.8871 (mm) cc_final: 0.8668 (mp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.4067 time to fit residues: 175.4505 Evaluate side-chains 187 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 348 optimal weight: 1.9990 chunk 366 optimal weight: 20.0000 chunk 334 optimal weight: 7.9990 chunk 356 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 322 optimal weight: 0.7980 chunk 337 optimal weight: 40.0000 chunk 355 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1028 ASN G1031 GLN ** G1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN F 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31861 Z= 0.229 Angle : 0.609 10.520 43336 Z= 0.328 Chirality : 0.042 0.163 4816 Planarity : 0.005 0.055 5634 Dihedral : 5.186 36.230 4371 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.31 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 3993 helix: 0.92 (0.19), residues: 723 sheet: -0.26 (0.16), residues: 914 loop : -0.47 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 553 HIS 0.005 0.001 HIS E 670 PHE 0.024 0.002 PHE A 850 TYR 0.017 0.002 TYR D 932 ARG 0.006 0.000 ARG D1057 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1036 LEU cc_start: 0.9764 (tp) cc_final: 0.9488 (tp) REVERT: A 1042 ASN cc_start: 0.8630 (t0) cc_final: 0.8362 (t0) REVERT: A 1084 GLN cc_start: 0.9355 (tp-100) cc_final: 0.9043 (tm-30) REVERT: B 3 GLN cc_start: 0.8708 (pt0) cc_final: 0.8397 (pm20) REVERT: B 28 THR cc_start: 0.8261 (m) cc_final: 0.7874 (p) REVERT: B 36 TRP cc_start: 0.8788 (m100) cc_final: 0.6870 (m100) REVERT: B 56 ASN cc_start: 0.8480 (t0) cc_final: 0.8243 (t0) REVERT: B 80 MET cc_start: 0.8816 (ttm) cc_final: 0.8236 (tmm) REVERT: C 62 PHE cc_start: 0.8686 (m-80) cc_final: 0.8403 (m-80) REVERT: C 85 MET cc_start: 0.9000 (mmm) cc_final: 0.8504 (mmm) REVERT: D 839 ASN cc_start: 0.9326 (m-40) cc_final: 0.8724 (m-40) REVERT: D 943 MET cc_start: 0.8667 (mmm) cc_final: 0.8382 (tpt) REVERT: D 977 PHE cc_start: 0.8878 (m-80) cc_final: 0.8459 (m-10) REVERT: D 1001 PHE cc_start: 0.9343 (t80) cc_final: 0.8900 (t80) REVERT: D 1067 ILE cc_start: 0.9579 (mt) cc_final: 0.9129 (tt) REVERT: G 757 MET cc_start: 0.8997 (mmt) cc_final: 0.8686 (mmt) REVERT: G 939 MET cc_start: 0.8556 (tpt) cc_final: 0.7873 (tpp) REVERT: G 943 MET cc_start: 0.9437 (mtp) cc_final: 0.8700 (mmm) REVERT: G 1042 ASN cc_start: 0.9003 (t0) cc_final: 0.8780 (t0) REVERT: G 1084 GLN cc_start: 0.9453 (tp-100) cc_final: 0.9012 (tm-30) REVERT: H 2 VAL cc_start: 0.8844 (t) cc_final: 0.7938 (t) REVERT: H 31 ASP cc_start: 0.8851 (m-30) cc_final: 0.8476 (m-30) REVERT: I 32 PHE cc_start: 0.8853 (m-10) cc_final: 0.8264 (m-80) REVERT: I 49 SER cc_start: 0.8593 (m) cc_final: 0.8285 (t) REVERT: I 85 MET cc_start: 0.9179 (mpp) cc_final: 0.8413 (mpp) REVERT: I 103 LYS cc_start: 0.9371 (tttt) cc_final: 0.9143 (tttp) REVERT: E 240 MET cc_start: 0.8236 (mmm) cc_final: 0.7991 (mmm) REVERT: E 452 MET cc_start: 0.2265 (ttt) cc_final: 0.2052 (ttt) REVERT: E 638 LEU cc_start: 0.9383 (tp) cc_final: 0.9141 (tp) REVERT: E 704 TYR cc_start: 0.5173 (t80) cc_final: 0.4504 (t80) REVERT: F 49 ASP cc_start: 0.7088 (t0) cc_final: 0.6597 (t0) REVERT: F 71 TYR cc_start: 0.9065 (t80) cc_final: 0.8720 (t80) REVERT: F 278 MET cc_start: 0.8684 (mmp) cc_final: 0.8235 (mmp) REVERT: F 324 LEU cc_start: 0.9441 (mt) cc_final: 0.9219 (mt) REVERT: F 343 ASP cc_start: 0.8837 (m-30) cc_final: 0.8396 (p0) REVERT: F 589 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6607 (pm20) REVERT: F 700 ARG cc_start: 0.7048 (mtt90) cc_final: 0.6643 (mmm160) REVERT: F 725 GLU cc_start: 0.8931 (pm20) cc_final: 0.7829 (tp30) REVERT: J 148 MET cc_start: 0.9457 (ttm) cc_final: 0.9087 (tpp) REVERT: J 239 PHE cc_start: 0.8292 (m-80) cc_final: 0.8013 (m-80) REVERT: J 278 MET cc_start: 0.8150 (mmm) cc_final: 0.7917 (mmm) REVERT: J 523 TYR cc_start: 0.7179 (m-10) cc_final: 0.6530 (m-80) REVERT: J 696 MET cc_start: 0.5933 (mmm) cc_final: 0.5636 (mmm) REVERT: J 700 ARG cc_start: 0.4659 (mmt180) cc_final: 0.3983 (mmm160) REVERT: J 717 LEU cc_start: 0.8836 (mm) cc_final: 0.8625 (mp) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.4380 time to fit residues: 183.6797 Evaluate side-chains 190 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 234 optimal weight: 0.8980 chunk 377 optimal weight: 5.9990 chunk 230 optimal weight: 30.0000 chunk 178 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 chunk 395 optimal weight: 0.9990 chunk 364 optimal weight: 10.0000 chunk 314 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 243 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 HIS ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1028 ASN G1110 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN F 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 31861 Z= 0.188 Angle : 0.590 10.347 43336 Z= 0.316 Chirality : 0.042 0.339 4816 Planarity : 0.004 0.054 5634 Dihedral : 5.041 41.207 4371 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 3993 helix: 1.19 (0.20), residues: 712 sheet: -0.18 (0.16), residues: 916 loop : -0.43 (0.13), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 253 HIS 0.006 0.001 HIS E 681 PHE 0.040 0.002 PHE A1001 TYR 0.029 0.001 TYR I 28 ARG 0.006 0.000 ARG D1057 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1042 ASN cc_start: 0.8706 (t0) cc_final: 0.8356 (t0) REVERT: A 1084 GLN cc_start: 0.9330 (tp-100) cc_final: 0.8987 (tm-30) REVERT: B 3 GLN cc_start: 0.8737 (pt0) cc_final: 0.8397 (pm20) REVERT: B 28 THR cc_start: 0.8257 (m) cc_final: 0.7827 (p) REVERT: B 36 TRP cc_start: 0.8742 (m100) cc_final: 0.6760 (m100) REVERT: B 56 ASN cc_start: 0.8459 (t0) cc_final: 0.8224 (t0) REVERT: B 80 MET cc_start: 0.8776 (ttm) cc_final: 0.8219 (tmm) REVERT: C 62 PHE cc_start: 0.8667 (m-80) cc_final: 0.8410 (m-80) REVERT: C 85 MET cc_start: 0.9040 (mmm) cc_final: 0.8525 (mmm) REVERT: D 771 ASP cc_start: 0.8961 (m-30) cc_final: 0.8734 (t0) REVERT: D 839 ASN cc_start: 0.9289 (m-40) cc_final: 0.8708 (m-40) REVERT: D 943 MET cc_start: 0.8631 (mmm) cc_final: 0.8395 (tpt) REVERT: D 977 PHE cc_start: 0.8895 (m-80) cc_final: 0.8460 (m-10) REVERT: D 1001 PHE cc_start: 0.9317 (t80) cc_final: 0.8858 (t80) REVERT: D 1067 ILE cc_start: 0.9568 (mt) cc_final: 0.9098 (tt) REVERT: D 1136 PHE cc_start: 0.9163 (m-80) cc_final: 0.8809 (m-10) REVERT: G 757 MET cc_start: 0.8950 (mmt) cc_final: 0.8700 (mmt) REVERT: G 843 ASP cc_start: 0.9305 (p0) cc_final: 0.9002 (p0) REVERT: G 909 TYR cc_start: 0.8090 (t80) cc_final: 0.7682 (t80) REVERT: G 939 MET cc_start: 0.8519 (tpt) cc_final: 0.7975 (tpp) REVERT: G 943 MET cc_start: 0.9413 (mtp) cc_final: 0.8686 (mmm) REVERT: G 1042 ASN cc_start: 0.8975 (t0) cc_final: 0.8763 (t0) REVERT: G 1084 GLN cc_start: 0.9443 (tp-100) cc_final: 0.8973 (tm-30) REVERT: H 2 VAL cc_start: 0.8831 (t) cc_final: 0.7662 (t) REVERT: H 31 ASP cc_start: 0.8831 (m-30) cc_final: 0.8443 (m-30) REVERT: H 69 MET cc_start: 0.7380 (ttt) cc_final: 0.5808 (ttt) REVERT: H 80 MET cc_start: 0.9085 (ttp) cc_final: 0.8670 (tpp) REVERT: I 32 PHE cc_start: 0.8895 (m-10) cc_final: 0.8338 (m-80) REVERT: I 45 LYS cc_start: 0.9319 (mmpt) cc_final: 0.9096 (mmmt) REVERT: I 46 LEU cc_start: 0.9222 (tt) cc_final: 0.8997 (tp) REVERT: I 49 SER cc_start: 0.8514 (m) cc_final: 0.8202 (t) REVERT: I 85 MET cc_start: 0.9174 (mpp) cc_final: 0.8402 (mpp) REVERT: I 103 LYS cc_start: 0.9482 (tttt) cc_final: 0.9142 (tttp) REVERT: I 104 LEU cc_start: 0.8721 (tp) cc_final: 0.8475 (tt) REVERT: E 240 MET cc_start: 0.8275 (mmm) cc_final: 0.8018 (mmm) REVERT: E 452 MET cc_start: 0.2211 (ttt) cc_final: 0.2007 (ttt) REVERT: E 563 MET cc_start: 0.1458 (ptp) cc_final: 0.0695 (tpt) REVERT: E 704 TYR cc_start: 0.5046 (t80) cc_final: 0.4317 (t80) REVERT: F 49 ASP cc_start: 0.7211 (t0) cc_final: 0.6647 (t0) REVERT: F 71 TYR cc_start: 0.9018 (t80) cc_final: 0.8717 (t80) REVERT: F 278 MET cc_start: 0.8667 (mmp) cc_final: 0.8237 (mmp) REVERT: F 324 LEU cc_start: 0.9388 (mt) cc_final: 0.9151 (mt) REVERT: F 343 ASP cc_start: 0.8802 (m-30) cc_final: 0.8372 (p0) REVERT: F 589 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6634 (pm20) REVERT: F 700 ARG cc_start: 0.6993 (mtt90) cc_final: 0.6537 (mmm160) REVERT: F 725 GLU cc_start: 0.8915 (pm20) cc_final: 0.7824 (tp30) REVERT: J 148 MET cc_start: 0.9473 (ttm) cc_final: 0.9125 (tpp) REVERT: J 278 MET cc_start: 0.8092 (mmm) cc_final: 0.7841 (mmm) REVERT: J 523 TYR cc_start: 0.7171 (m-10) cc_final: 0.6574 (m-80) REVERT: J 696 MET cc_start: 0.5877 (mmm) cc_final: 0.5577 (mmm) REVERT: J 700 ARG cc_start: 0.4659 (mmt180) cc_final: 0.4015 (mmm160) REVERT: J 717 LEU cc_start: 0.8818 (mm) cc_final: 0.8609 (mp) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3997 time to fit residues: 172.7018 Evaluate side-chains 193 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 250 optimal weight: 4.9990 chunk 335 optimal weight: 0.0030 chunk 96 optimal weight: 0.1980 chunk 290 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 315 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 323 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN A1122 HIS ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1104 ASN ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN F 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.067857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051053 restraints weight = 218847.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.052318 restraints weight = 135261.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.053186 restraints weight = 95982.978| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 31861 Z= 0.144 Angle : 0.566 10.573 43336 Z= 0.300 Chirality : 0.042 0.240 4816 Planarity : 0.004 0.053 5634 Dihedral : 4.695 38.771 4371 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.16 % Favored : 94.62 % Rotamer: Outliers : 0.03 % Allowed : 0.12 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 3993 helix: 1.56 (0.20), residues: 712 sheet: -0.02 (0.16), residues: 928 loop : -0.35 (0.13), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 47 HIS 0.005 0.001 HIS D1122 PHE 0.020 0.001 PHE C 62 TYR 0.033 0.001 TYR D 947 ARG 0.008 0.000 ARG B 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5688.36 seconds wall clock time: 104 minutes 54.69 seconds (6294.69 seconds total)