Starting phenix.real_space_refine on Sat Feb 17 02:38:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/02_2024/7scn_25039.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/02_2024/7scn_25039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/02_2024/7scn_25039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/02_2024/7scn_25039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/02_2024/7scn_25039.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/02_2024/7scn_25039.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 10806 2.51 5 N 2919 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17145 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "B" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "I" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "J" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 9.63, per 1000 atoms: 0.56 Number of scatterers: 17145 At special positions: 0 Unit cell: (124.2, 129.95, 147.2, 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 78 16.00 O 3342 8.00 N 2919 7.00 C 10806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.05 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS H 529 " - pdb=" SG CYS H 602 " distance=2.01 Simple disulfide: pdb=" SG CYS L 646 " - pdb=" SG CYS L 712 " distance=2.02 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 467 " distance=2.04 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.05 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.05 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 529 " - pdb=" SG CYS E 602 " distance=2.01 Simple disulfide: pdb=" SG CYS F 646 " - pdb=" SG CYS F 712 " distance=2.02 Simple disulfide: pdb=" SG CYS G 8 " - pdb=" SG CYS I 467 " distance=2.04 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 278 " distance=2.05 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 71 " distance=2.02 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 139 " distance=2.05 Simple disulfide: pdb=" SG CYS G 282 " - pdb=" SG CYS G 306 " distance=2.02 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS J 529 " - pdb=" SG CYS J 602 " distance=2.01 Simple disulfide: pdb=" SG CYS K 646 " - pdb=" SG CYS K 712 " distance=2.02 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 58 " " NAG A 402 " - " ASN A 27 " " NAG A 403 " - " ASN A 91 " " NAG A 404 " - " ASN A 129 " " NAG A 405 " - " ASN A 290 " " NAG C 401 " - " ASN C 58 " " NAG C 402 " - " ASN C 27 " " NAG C 403 " - " ASN C 91 " " NAG C 404 " - " ASN C 129 " " NAG C 405 " - " ASN C 290 " " NAG G 401 " - " ASN G 58 " " NAG G 402 " - " ASN G 27 " " NAG G 403 " - " ASN G 91 " " NAG G 404 " - " ASN G 129 " " NAG G 405 " - " ASN G 290 " Time building additional restraints: 6.59 Conformation dependent library (CDL) restraints added in 2.8 seconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 22.4% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.899A pdb=" N GLU A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU A 73 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.340A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 367 through 389 Processing helix chain 'B' and resid 404 through 457 removed outlier: 4.028A pdb=" N GLN B 455 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 488 through 503 removed outlier: 3.826A pdb=" N TYR B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 535 through 539 Processing helix chain 'H' and resid 568 through 571 Processing helix chain 'L' and resid 653 through 655 No H-bonds generated for 'chain 'L' and resid 653 through 655' Processing helix chain 'L' and resid 703 through 707 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.898A pdb=" N GLU C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU C 73 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.341A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 367 through 389 Processing helix chain 'D' and resid 404 through 457 removed outlier: 4.027A pdb=" N GLN D 455 " --> pdb=" O LYS D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 488 through 503 removed outlier: 3.827A pdb=" N TYR D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU D 494 " --> pdb=" O PRO D 490 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU D 495 " --> pdb=" O LYS D 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 568 through 571 Processing helix chain 'F' and resid 653 through 655 No H-bonds generated for 'chain 'F' and resid 653 through 655' Processing helix chain 'F' and resid 703 through 707 Processing helix chain 'G' and resid 60 through 67 Processing helix chain 'G' and resid 68 through 75 removed outlier: 3.898A pdb=" N GLU G 72 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU G 73 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 122 through 127 removed outlier: 4.340A pdb=" N TRP G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 195 Processing helix chain 'I' and resid 367 through 389 Processing helix chain 'I' and resid 404 through 457 removed outlier: 4.027A pdb=" N GLN I 455 " --> pdb=" O LYS I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 Processing helix chain 'I' and resid 488 through 503 removed outlier: 3.827A pdb=" N TYR I 492 " --> pdb=" O ASP I 488 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU I 494 " --> pdb=" O PRO I 490 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU I 495 " --> pdb=" O LYS I 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 535 through 539 Processing helix chain 'J' and resid 568 through 571 Processing helix chain 'K' and resid 653 through 655 No H-bonds generated for 'chain 'K' and resid 653 through 655' Processing helix chain 'K' and resid 703 through 707 Processing sheet with id=AA1, first strand: chain 'B' and resid 361 through 366 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 48 removed outlier: 6.257A pdb=" N LEU A 45 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.658A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A 115 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA A 259 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 117 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 257 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A 115 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA A 259 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 117 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 257 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.726A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.137A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 512 through 513 Processing sheet with id=AB4, first strand: chain 'H' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU H 517 " --> pdb=" O THR H 624 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE H 541 " --> pdb=" O ARG H 557 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG H 557 " --> pdb=" O PHE H 541 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 543 " --> pdb=" O MET H 555 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU H 517 " --> pdb=" O THR H 624 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 627 through 630 Processing sheet with id=AB7, first strand: chain 'L' and resid 633 through 636 removed outlier: 6.707A pdb=" N LEU L 657 " --> pdb=" O TYR L 673 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR L 673 " --> pdb=" O LEU L 657 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 659 " --> pdb=" O LEU L 671 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 633 through 636 Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 366 Processing sheet with id=AC1, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.256A pdb=" N LEU C 45 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N CYS C 278 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.660A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER C 261 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 115 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA C 259 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 117 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 257 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER C 261 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 115 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA C 259 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 117 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 257 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.725A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD1, first strand: chain 'C' and resid 287 through 289 removed outlier: 4.136A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 512 through 513 Processing sheet with id=AD3, first strand: chain 'E' and resid 517 through 518 removed outlier: 6.655A pdb=" N GLU E 517 " --> pdb=" O THR E 624 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE E 541 " --> pdb=" O ARG E 557 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG E 557 " --> pdb=" O PHE E 541 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP E 543 " --> pdb=" O MET E 555 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 517 through 518 removed outlier: 6.655A pdb=" N GLU E 517 " --> pdb=" O THR E 624 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 627 through 630 Processing sheet with id=AD6, first strand: chain 'F' and resid 633 through 636 removed outlier: 6.707A pdb=" N LEU F 657 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR F 673 " --> pdb=" O LEU F 657 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP F 659 " --> pdb=" O LEU F 671 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 633 through 636 Processing sheet with id=AD8, first strand: chain 'I' and resid 361 through 366 Processing sheet with id=AD9, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AE2, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AE3, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.256A pdb=" N LEU G 45 " --> pdb=" O ASP G 276 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N CYS G 278 " --> pdb=" O LEU G 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.659A pdb=" N LEU G 54 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER G 261 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 115 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA G 259 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG G 117 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA G 257 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER G 261 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 115 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA G 259 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG G 117 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA G 257 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 136 through 141 removed outlier: 4.726A pdb=" N CYS G 139 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER G 146 " --> pdb=" O CYS G 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE9, first strand: chain 'G' and resid 287 through 289 removed outlier: 4.136A pdb=" N CYS G 282 " --> pdb=" O ILE G 289 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 512 through 513 Processing sheet with id=AF2, first strand: chain 'J' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU J 517 " --> pdb=" O THR J 624 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE J 541 " --> pdb=" O ARG J 557 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG J 557 " --> pdb=" O PHE J 541 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP J 543 " --> pdb=" O MET J 555 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU J 517 " --> pdb=" O THR J 624 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 627 through 630 Processing sheet with id=AF5, first strand: chain 'K' and resid 633 through 636 removed outlier: 6.707A pdb=" N LEU K 657 " --> pdb=" O TYR K 673 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR K 673 " --> pdb=" O LEU K 657 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP K 659 " --> pdb=" O LEU K 671 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 633 through 636 741 hydrogen bonds defined for protein. 1926 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: 7.39 Time building geometry restraints manager: 7.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5141 1.33 - 1.48: 5396 1.48 - 1.62: 6887 1.62 - 1.76: 36 1.76 - 1.90: 93 Bond restraints: 17553 Sorted by residual: bond pdb=" CB ILE I 503 " pdb=" CG1 ILE I 503 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" CB ILE D 503 " pdb=" CG1 ILE D 503 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CB ILE B 503 " pdb=" CG1 ILE B 503 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" CB ILE B 336 " pdb=" CG1 ILE B 336 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CB ILE D 336 " pdb=" CG1 ILE D 336 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 17548 not shown) Histogram of bond angle deviations from ideal: 90.54 - 104.11: 273 104.11 - 117.67: 12655 117.67 - 131.23: 10825 131.23 - 144.79: 67 144.79 - 158.35: 3 Bond angle restraints: 23823 Sorted by residual: angle pdb=" N TYR H 609 " pdb=" CA TYR H 609 " pdb=" C TYR H 609 " ideal model delta sigma weight residual 113.12 90.54 22.58 1.25e+00 6.40e-01 3.26e+02 angle pdb=" N TYR E 609 " pdb=" CA TYR E 609 " pdb=" C TYR E 609 " ideal model delta sigma weight residual 113.12 90.57 22.55 1.25e+00 6.40e-01 3.25e+02 angle pdb=" N TYR J 609 " pdb=" CA TYR J 609 " pdb=" C TYR J 609 " ideal model delta sigma weight residual 113.12 90.58 22.54 1.25e+00 6.40e-01 3.25e+02 angle pdb=" C2 NAG G 404 " pdb=" N2 NAG G 404 " pdb=" C7 NAG G 404 " ideal model delta sigma weight residual 124.56 158.35 -33.79 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C2 NAG C 404 " pdb=" N2 NAG C 404 " pdb=" C7 NAG C 404 " ideal model delta sigma weight residual 124.56 158.32 -33.76 3.00e+00 1.11e-01 1.27e+02 ... (remaining 23818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 10222 17.16 - 34.32: 272 34.32 - 51.48: 69 51.48 - 68.64: 46 68.64 - 85.80: 17 Dihedral angle restraints: 10626 sinusoidal: 4434 harmonic: 6192 Sorted by residual: dihedral pdb=" CB CYS D 474 " pdb=" SG CYS D 474 " pdb=" SG CYS D 478 " pdb=" CB CYS D 478 " ideal model delta sinusoidal sigma weight residual 93.00 146.18 -53.18 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CB CYS B 474 " pdb=" SG CYS B 474 " pdb=" SG CYS B 478 " pdb=" CB CYS B 478 " ideal model delta sinusoidal sigma weight residual 93.00 146.15 -53.15 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CB CYS I 474 " pdb=" SG CYS I 474 " pdb=" SG CYS I 478 " pdb=" CB CYS I 478 " ideal model delta sinusoidal sigma weight residual 93.00 146.14 -53.14 1 1.00e+01 1.00e-02 3.84e+01 ... (remaining 10623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1883 0.100 - 0.199: 555 0.199 - 0.299: 111 0.299 - 0.398: 32 0.398 - 0.498: 26 Chirality restraints: 2607 Sorted by residual: chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 3.14 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CB ILE D 336 " pdb=" CA ILE D 336 " pdb=" CG1 ILE D 336 " pdb=" CG2 ILE D 336 " both_signs ideal model delta sigma weight residual False 2.64 3.14 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CB ILE I 336 " pdb=" CA ILE I 336 " pdb=" CG1 ILE I 336 " pdb=" CG2 ILE I 336 " both_signs ideal model delta sigma weight residual False 2.64 3.14 -0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 2604 not shown) Planarity restraints: 3078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 449 " 0.063 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR D 449 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 449 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR D 449 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 449 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR D 449 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 449 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 449 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 449 " -0.062 2.00e-02 2.50e+03 3.44e-02 2.36e+01 pdb=" CG TYR B 449 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 449 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 449 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 449 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR B 449 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR B 449 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 449 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 449 " -0.062 2.00e-02 2.50e+03 3.44e-02 2.36e+01 pdb=" CG TYR I 449 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR I 449 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR I 449 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR I 449 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR I 449 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR I 449 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 449 " -0.053 2.00e-02 2.50e+03 ... (remaining 3075 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 3 1.89 - 2.64: 321 2.64 - 3.40: 21609 3.40 - 4.15: 44659 4.15 - 4.90: 76626 Nonbonded interactions: 143218 Sorted by model distance: nonbonded pdb=" NE2 GLN L 714 " pdb=" CG2 THR L 721 " model vdw 1.142 3.540 nonbonded pdb=" CD1 LEU L 627 " pdb=" OE1 GLN L 714 " model vdw 1.750 3.460 nonbonded pdb=" CD GLN L 714 " pdb=" CG2 THR L 721 " model vdw 1.786 3.690 nonbonded pdb=" NE2 GLN B 372 " pdb=" OG SER H 607 " model vdw 2.099 2.520 nonbonded pdb=" N TYR E 609 " pdb=" N PHE E 610 " model vdw 2.215 2.560 ... (remaining 143213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.030 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 47.590 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.022 0.166 17553 Z= 1.417 Angle : 1.786 33.790 23823 Z= 1.182 Chirality : 0.109 0.498 2607 Planarity : 0.009 0.055 3063 Dihedral : 10.402 85.803 6606 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2121 helix: 1.24 (0.24), residues: 363 sheet: 1.19 (0.23), residues: 504 loop : 0.65 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.008 TRP H 554 HIS 0.013 0.003 HIS I 472 PHE 0.035 0.007 PHE F 722 TYR 0.063 0.009 TYR D 449 ARG 0.009 0.001 ARG J 619 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 422 time to evaluate : 2.131 Fit side-chains REVERT: A 275 MET cc_start: 0.8103 (tpt) cc_final: 0.7746 (tpt) REVERT: H 587 MET cc_start: 0.8019 (ttp) cc_final: 0.7807 (ttp) REVERT: D 347 MET cc_start: 0.8308 (ttp) cc_final: 0.7922 (ttm) REVERT: F 701 ARG cc_start: 0.6949 (mtm-85) cc_final: 0.6598 (mtm-85) REVERT: G 222 LYS cc_start: 0.9018 (mttt) cc_final: 0.8805 (mttm) REVERT: I 347 MET cc_start: 0.8207 (ttp) cc_final: 0.7832 (ttm) REVERT: I 484 ASN cc_start: 0.7638 (m-40) cc_final: 0.7378 (m110) REVERT: K 630 SER cc_start: 0.6884 (t) cc_final: 0.6600 (p) outliers start: 3 outliers final: 3 residues processed: 425 average time/residue: 0.3389 time to fit residues: 207.7368 Evaluate side-chains 231 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain G residue 115 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 55 GLN C 296 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 296 GLN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17553 Z= 0.223 Angle : 0.604 9.136 23823 Z= 0.330 Chirality : 0.047 0.251 2607 Planarity : 0.004 0.033 3063 Dihedral : 6.308 81.543 2661 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.15 % Allowed : 6.89 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.27 (0.18), residues: 2121 helix: 2.29 (0.25), residues: 369 sheet: 0.73 (0.20), residues: 627 loop : 0.54 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 720 HIS 0.004 0.001 HIS G 41 PHE 0.018 0.002 PHE L 722 TYR 0.015 0.002 TYR K 710 ARG 0.005 0.001 ARG H 619 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 269 time to evaluate : 1.894 Fit side-chains revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8262 (m-70) cc_final: 0.7847 (m-70) REVERT: A 317 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8182 (ttt) REVERT: B 396 VAL cc_start: 0.7869 (t) cc_final: 0.7418 (p) REVERT: D 347 MET cc_start: 0.8200 (ttp) cc_final: 0.7735 (ttm) REVERT: E 587 MET cc_start: 0.7826 (ttp) cc_final: 0.7245 (ttp) REVERT: I 347 MET cc_start: 0.8149 (ttp) cc_final: 0.7850 (ttm) REVERT: J 580 LYS cc_start: 0.9029 (ptmm) cc_final: 0.8781 (ptmt) outliers start: 40 outliers final: 23 residues processed: 291 average time/residue: 0.3066 time to fit residues: 135.1158 Evaluate side-chains 256 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain H residue 621 THR Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 645 SER Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 624 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 402 LYS Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 186 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 376 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17553 Z= 0.197 Angle : 0.537 9.495 23823 Z= 0.289 Chirality : 0.044 0.239 2607 Planarity : 0.004 0.034 3063 Dihedral : 5.854 79.997 2661 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.99 % Allowed : 8.62 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 1.18 (0.18), residues: 2121 helix: 2.58 (0.26), residues: 369 sheet: 0.52 (0.20), residues: 645 loop : 0.45 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 554 HIS 0.003 0.001 HIS A 12 PHE 0.017 0.002 PHE C 115 TYR 0.017 0.002 TYR E 609 ARG 0.006 0.000 ARG E 619 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 257 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8305 (m-70) cc_final: 0.7907 (m-70) REVERT: A 317 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8098 (ttt) REVERT: B 396 VAL cc_start: 0.7957 (t) cc_final: 0.7486 (p) REVERT: H 571 ARG cc_start: 0.7420 (mtt90) cc_final: 0.6952 (mtt90) REVERT: E 587 MET cc_start: 0.7835 (ttp) cc_final: 0.7194 (ttp) REVERT: I 347 MET cc_start: 0.8139 (ttp) cc_final: 0.7608 (ttm) REVERT: J 580 LYS cc_start: 0.9012 (ptmm) cc_final: 0.8708 (ptmt) outliers start: 37 outliers final: 26 residues processed: 276 average time/residue: 0.2916 time to fit residues: 121.2377 Evaluate side-chains 256 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 621 THR Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 402 LYS Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 698 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 713 GLN ** K 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17553 Z= 0.178 Angle : 0.517 8.852 23823 Z= 0.274 Chirality : 0.044 0.190 2607 Planarity : 0.004 0.041 3063 Dihedral : 5.848 82.028 2661 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.21 % Allowed : 9.48 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.25 (0.18), residues: 2121 helix: 2.85 (0.26), residues: 369 sheet: 0.65 (0.22), residues: 582 loop : 0.35 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.004 0.001 HIS G 130 PHE 0.016 0.002 PHE A 115 TYR 0.014 0.002 TYR F 673 ARG 0.009 0.000 ARG E 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 254 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8359 (m-70) cc_final: 0.7993 (m-70) REVERT: B 396 VAL cc_start: 0.7990 (t) cc_final: 0.7514 (p) REVERT: H 571 ARG cc_start: 0.7478 (mtt90) cc_final: 0.6970 (mtt90) REVERT: E 587 MET cc_start: 0.7746 (ttp) cc_final: 0.7123 (ttp) REVERT: I 347 MET cc_start: 0.8147 (ttp) cc_final: 0.7753 (ttm) REVERT: I 349 ASP cc_start: 0.7779 (p0) cc_final: 0.7558 (p0) REVERT: J 580 LYS cc_start: 0.8979 (ptmm) cc_final: 0.8690 (ptmt) REVERT: J 608 MET cc_start: 0.6419 (tpp) cc_final: 0.6106 (tpt) outliers start: 41 outliers final: 28 residues processed: 276 average time/residue: 0.2904 time to fit residues: 121.5155 Evaluate side-chains 258 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 230 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain L residue 626 VAL Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN C 231 ASN D 372 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 HIS G 231 ASN ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 713 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 17553 Z= 0.439 Angle : 0.663 10.090 23823 Z= 0.346 Chirality : 0.049 0.200 2607 Planarity : 0.005 0.052 3063 Dihedral : 6.497 80.274 2661 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.96 % Allowed : 9.85 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.80 (0.18), residues: 2121 helix: 2.46 (0.26), residues: 369 sheet: 0.51 (0.20), residues: 609 loop : -0.04 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 581 HIS 0.008 0.002 HIS A 12 PHE 0.018 0.002 PHE C 99 TYR 0.020 0.002 TYR E 609 ARG 0.006 0.001 ARG H 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 252 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8533 (m-70) cc_final: 0.8271 (m-70) REVERT: A 317 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8203 (ttt) REVERT: H 565 ASP cc_start: 0.7540 (t0) cc_final: 0.7306 (t0) REVERT: H 571 ARG cc_start: 0.7600 (mtt90) cc_final: 0.7182 (mtt90) REVERT: C 120 ILE cc_start: 0.8555 (mt) cc_final: 0.8334 (mt) REVERT: E 587 MET cc_start: 0.8056 (ttp) cc_final: 0.7346 (ttp) REVERT: F 660 TYR cc_start: 0.8068 (m-80) cc_final: 0.7764 (m-80) outliers start: 55 outliers final: 42 residues processed: 282 average time/residue: 0.3133 time to fit residues: 131.3974 Evaluate side-chains 282 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 607 SER Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain L residue 626 VAL Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain E residue 624 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS C 41 HIS C 248 ASN D 356 HIS ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 355 HIS I 372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17553 Z= 0.204 Angle : 0.533 10.648 23823 Z= 0.281 Chirality : 0.044 0.183 2607 Planarity : 0.004 0.038 3063 Dihedral : 6.152 81.128 2661 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.21 % Allowed : 10.99 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.98 (0.18), residues: 2121 helix: 2.81 (0.26), residues: 369 sheet: 0.48 (0.21), residues: 612 loop : 0.10 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.009 0.001 HIS D 356 PHE 0.016 0.002 PHE C 115 TYR 0.017 0.002 TYR K 673 ARG 0.006 0.000 ARG H 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8474 (m-70) cc_final: 0.8195 (m-70) REVERT: E 587 MET cc_start: 0.7812 (ttp) cc_final: 0.7220 (ttp) REVERT: J 608 MET cc_start: 0.6494 (tpp) cc_final: 0.6262 (tpt) outliers start: 41 outliers final: 34 residues processed: 267 average time/residue: 0.2884 time to fit residues: 116.9492 Evaluate side-chains 264 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 230 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 698 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17553 Z= 0.217 Angle : 0.533 9.289 23823 Z= 0.280 Chirality : 0.043 0.180 2607 Planarity : 0.004 0.035 3063 Dihedral : 5.910 80.873 2661 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.69 % Allowed : 11.63 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.98 (0.18), residues: 2121 helix: 2.84 (0.26), residues: 372 sheet: 0.46 (0.21), residues: 612 loop : 0.09 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 422 HIS 0.004 0.001 HIS A 12 PHE 0.015 0.002 PHE C 115 TYR 0.015 0.002 TYR K 715 ARG 0.004 0.000 ARG H 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 230 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8461 (m-70) cc_final: 0.8160 (m-70) REVERT: H 571 ARG cc_start: 0.7455 (mtt90) cc_final: 0.6977 (mtt90) REVERT: C 248 ASN cc_start: 0.8074 (m-40) cc_final: 0.7666 (m-40) REVERT: C 276 ASP cc_start: 0.6355 (p0) cc_final: 0.6083 (p0) REVERT: E 587 MET cc_start: 0.7876 (ttp) cc_final: 0.7270 (ttp) REVERT: J 608 MET cc_start: 0.6780 (tpp) cc_final: 0.6530 (tpt) outliers start: 50 outliers final: 42 residues processed: 260 average time/residue: 0.2736 time to fit residues: 109.9877 Evaluate side-chains 267 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain L residue 626 VAL Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 445 VAL Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 60 optimal weight: 0.0470 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17553 Z= 0.185 Angle : 0.515 9.910 23823 Z= 0.271 Chirality : 0.043 0.181 2607 Planarity : 0.004 0.034 3063 Dihedral : 5.706 81.423 2661 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.96 % Allowed : 11.47 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.07 (0.18), residues: 2121 helix: 2.99 (0.26), residues: 372 sheet: 0.50 (0.21), residues: 612 loop : 0.13 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 543 HIS 0.002 0.001 HIS A 12 PHE 0.015 0.002 PHE C 115 TYR 0.015 0.001 TYR F 673 ARG 0.007 0.000 ARG E 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 230 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8451 (m-70) cc_final: 0.8143 (m-70) REVERT: H 571 ARG cc_start: 0.7484 (mtt90) cc_final: 0.7019 (mtt90) REVERT: C 75 ILE cc_start: 0.8749 (pt) cc_final: 0.8333 (pt) REVERT: E 587 MET cc_start: 0.7792 (ttp) cc_final: 0.7175 (ttp) REVERT: J 553 GLU cc_start: 0.8017 (tt0) cc_final: 0.7715 (tt0) REVERT: J 608 MET cc_start: 0.6680 (tpp) cc_final: 0.6463 (tpt) outliers start: 55 outliers final: 45 residues processed: 265 average time/residue: 0.2870 time to fit residues: 115.9793 Evaluate side-chains 269 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain L residue 626 VAL Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 698 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 698 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 445 VAL Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.9990 chunk 191 optimal weight: 0.4980 chunk 174 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 0.0770 chunk 57 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 122 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17553 Z= 0.161 Angle : 0.516 12.313 23823 Z= 0.269 Chirality : 0.043 0.181 2607 Planarity : 0.004 0.035 3063 Dihedral : 5.970 81.384 2661 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.37 % Allowed : 11.95 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.14 (0.18), residues: 2121 helix: 3.10 (0.26), residues: 372 sheet: 0.54 (0.21), residues: 612 loop : 0.16 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 351 HIS 0.004 0.001 HIS G 130 PHE 0.015 0.001 PHE C 115 TYR 0.017 0.001 TYR F 673 ARG 0.009 0.000 ARG F 685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8429 (m-70) cc_final: 0.8132 (m-70) REVERT: B 396 VAL cc_start: 0.8149 (t) cc_final: 0.7640 (p) REVERT: C 75 ILE cc_start: 0.8767 (pt) cc_final: 0.8357 (pt) REVERT: E 587 MET cc_start: 0.7687 (ttp) cc_final: 0.7071 (ttp) REVERT: F 685 ARG cc_start: 0.6262 (ttp-110) cc_final: 0.5890 (ttp-110) REVERT: J 553 GLU cc_start: 0.7999 (tt0) cc_final: 0.7692 (tt0) REVERT: J 608 MET cc_start: 0.6660 (tpp) cc_final: 0.6443 (tpt) outliers start: 44 outliers final: 37 residues processed: 266 average time/residue: 0.2909 time to fit residues: 117.7353 Evaluate side-chains 269 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 561 ILE Chi-restraints excluded: chain L residue 626 VAL Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 445 VAL Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17553 Z= 0.364 Angle : 0.631 10.450 23823 Z= 0.325 Chirality : 0.047 0.188 2607 Planarity : 0.005 0.037 3063 Dihedral : 6.486 80.777 2661 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.42 % Allowed : 12.06 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.82 (0.18), residues: 2121 helix: 2.72 (0.26), residues: 369 sheet: 0.41 (0.21), residues: 612 loop : -0.05 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 581 HIS 0.007 0.001 HIS A 12 PHE 0.015 0.002 PHE A 115 TYR 0.015 0.002 TYR H 601 ARG 0.007 0.001 ARG E 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 232 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8555 (m-70) cc_final: 0.8325 (m-70) REVERT: L 636 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7259 (mp) REVERT: C 75 ILE cc_start: 0.8815 (pt) cc_final: 0.8398 (pt) REVERT: E 587 MET cc_start: 0.8169 (ttp) cc_final: 0.7509 (ttp) REVERT: G 311 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.8095 (mtm180) outliers start: 45 outliers final: 41 residues processed: 263 average time/residue: 0.2882 time to fit residues: 116.0089 Evaluate side-chains 272 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain L residue 626 VAL Chi-restraints excluded: chain L residue 628 THR Chi-restraints excluded: chain L residue 636 LEU Chi-restraints excluded: chain L residue 709 VAL Chi-restraints excluded: chain L residue 721 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 115 PHE Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 443 SER Chi-restraints excluded: chain I residue 445 VAL Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 597 THR Chi-restraints excluded: chain K residue 626 VAL Chi-restraints excluded: chain K residue 628 THR Chi-restraints excluded: chain K residue 698 THR Chi-restraints excluded: chain K residue 709 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.163692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134995 restraints weight = 20756.712| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.60 r_work: 0.3260 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17553 Z= 0.195 Angle : 0.535 10.543 23823 Z= 0.278 Chirality : 0.043 0.212 2607 Planarity : 0.004 0.036 3063 Dihedral : 6.199 81.821 2661 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.26 % Allowed : 12.17 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.18), residues: 2121 helix: 2.93 (0.26), residues: 372 sheet: 0.38 (0.21), residues: 618 loop : 0.07 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 581 HIS 0.003 0.001 HIS A 12 PHE 0.015 0.002 PHE C 115 TYR 0.015 0.001 TYR K 673 ARG 0.007 0.000 ARG E 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3851.43 seconds wall clock time: 70 minutes 57.75 seconds (4257.75 seconds total)